Jones and Thome were both elected in their first year of eligibility. This is the fourth time that the Baseball Writers' Association of America has elected four players in a year (1947, 1955, 2015).
"It was waterworks," said Jones, who drew 97.2 percent of the vote after being selected on 410 of 422 ballots.
The four will join veterans committee inductees Jack Morris and Alan Trammell in entering the Baseball Hall of Fame on July 29 in Cooperstown, New York.
It took 75 percent for election, or 317 votes, to be elected into the Hall of Fame. Designated hitter Edgar Martinez came close -- falling just 20 votes shy -- after a grass-roots campaign. Roger Clemens, who was picked on 57.3 percent of ballots, and Barry Bonds (56.4), both tainted by the steroids scandal, edged up in voting totals but again fell far short.
Jones, an eight-time All-Star who played all 19 seasons for the Atlanta Braves, ranks third all time in home runs by a switch-hitter. The veteran third baseman had a career .303 batting average with 468 home runs.
He is the only switch-hitter with at least 1,000 at-bats and a .300 batting average, .400 on-base percentage and .500 slugging percentage.
"I don't know how you tabulate or calculate WAR,'' Jones said, referring to a sabermetric stat that didn't exist for much of his career. "... What I want to see is batting average, on-base percentage, runs produced.''
Jones, a force for most of the Atlanta teams that won 14 straight division titles, joins former teammates John Smoltz, Tom Glavine and Greg Maddux, manager Bobby Cox and general manager John Schuerholz in the Hall.
Of the four new members, Jones was the only one to win a World Series. He joins Ken Griffey Jr. as the only overall No. 1 draft picks to reach the Hall.
Thome hit 612 home runs, which ranks eighth all time, over his 22 seasons with the Indians, Phillies, White Sox, Twins, Dodgers and Orioles. The infielder's 13 walk-off home runs are more than any other player.
Thome became emotional after receiving a call from former manager Charlie Manuel, his longtime hitting coach, while he was being interviewed on MLB Network.
"I couldn't be happier for Jim, who is like a son to me," Manuel said. "This is totally deserving and, for me, ranks up there with anything I've ever seen happen in the game of baseball. For someone that I met as a 19-year-old and saw improve as much as anyone over time, it makes me smile to think that all that hard work, all those swings in the batting cage, is now paying off for him.
"I started thinking this was possible after he hit his 500th home run. And for the day to finally be here, it's like winning the World Series all over again."
Thome was known for his batter's box routine, standing absolutely still in the box while pointing his bat at the pitcher. He said the posture helped him relax, slow down and "not be so tense.''
Guerrero, a nine-time All-Star, was elected in his second try, getting 92.9 percent of the vote. Over his 16 seasons with the Montreal Expos, Angels, Rangers and Orioles, Guerrero had a .318 career batting average and a .553 slugging percentage -- one of nine players with numbers higher than .315/.550.
"I still can't believe it," Guerrero, the first position player from the Dominican Republic to make the Hall, told ESPN Deportes on Wednesday. "Maybe I have to wait until tomorrow to make sure this is for real. This is for Don Gregorio [his hometown], my people and the entire Dominican Republic."
Dominican Republic President Danilo Medina, who was in Switzerland, congratulated Guerrero on Twitter, saying "it fills all Dominicans with pride that he has carried our flag to the top.''
The outfielder, a notorious bad-ball hitter, also had 449 home runs and 1,496 RBIs. His career batting average is sixth highest among players with at least 400 career home runs.
Guerrero said he developed his hitting talent as a kid in the Dominican Republic, playing a game similar to cricket in which hitters swung broomsticks while pitchers tried to bounce balls past them and knock over folded license plates.
Thank you Baseball. pic.twitter.com/u6sUvlgiNu— Vladimir Guerrero (@VladGuerrero27) January 24, 2018
Hoffman, getting 79.9 percent of the vote to become just the sixth reliever to be elected into Cooperstown, has 601 career saves, which ranks second to Mariano Rivera on the all-time list. And his nine seasons with at least 40 saves are tied with Rivera for most all time.
"This was my job title, this is what I was asked to do, and I did it pretty well," Hoffman said at Petco Park in San Diego. "There's really not much else you can do [about making the Hall] after you're done playing. You can choose to kind of battle a fight that's not worth fighting.
"I was comfortable with the career I had, comfortable with the way I went about it, and if enough people felt the same about it as I did, we'd be standing here today. And fortunately, we were."
"Trevor Time" became an event in San Diego, where AC/DC's "Hells Bells" blared when batters knew they'd be facing Hoffman's flummoxing changeup, which dropped toward the dirt and more often than not eluded their bats.
"It was one of those moments in the game that never, never got old, trust me," said Bruce Bochy, who managed Hoffman in San Diego from 1995 to 2006, before becoming the Giants' manager. "It's always good to bring your closer in, but the 'Hells Bells' became part of it, just to see how it brought the crowd to life, the team. It energized the whole ballpark. It was electric."
Rivera highlights the newcomers on next year's ballot, once again raising debate over whether any player will be unanimously elected to the Hall. Todd Helton, Andy Pettitte and the late Roy Halladay also will be first-time candidates.
For Martinez, who finished with 70.4 percent of the vote in his ninth time on the ballot, it was the second straight year with a significant jump; he was at 58.6 percent in the 2017 voting.
Martinez remains optimistic about his chances in 2019.
"Getting 70.4 percent is a big improvement, and all I can think right now is that it's looking good for next year," Martinez said on a conference call. "It would have been great to get in this year, but it looks good for next year."
Just four years ago, Martinez was slogging at 25.2 percent in the balloting, but the past few years have marked a major change in how voters are viewing his contributions, even though he rarely played the field after 1992. Martinez's career .312 batting average, .933 on-base plus slugging and seven All-Star Game appearances created a strong foundation for his candidacy.
"At that time, I thought I would never get to this point," Martinez said. "It is encouraging to see 70 percent going into my final year. I just feel I still have a good chance. But yeah, 2014, I didn't think I was going to be at this point right now."
In addition to Martinez, Clemens and Bonds, pitchers Mike Mussina (63.5) and Curt Schilling (51.2) were named on more than half the ballots but were not elected.
Clemens and Bonds each get four more tries. They seem to be "gaining steam with newer voters,'' Jones said.
Omar Vizquel (37 percent), Scott Rolen (10.2) and Andruw Jones (7.3) were first-time candidates. Among the players who drew under 5 percent and fell off the ballot were Johnny Damon, Hideki Matsui and Johan Santana.
Pete Rose, permanently banned from Major League Baseball after an investigation into his betting on the game, didn't receive any write-in votes, as he often has in the past.
The Baseball Writers' Association of America has elected 16 players to the Hall over the past five years, the largest total over a five-year span, breaking the previous mark of 13 from 1952 to 1956.
The Associated Press contributed to this report.