The Padres also got right-hander Aaron Northcraft in the deal. Atlanta received minor league left-hander Max Fried, infielders Dustin Peterson and Jace Peterson, outfielder Mallex Smith and international bonus compensation.
Upton joins a Padres outfield that includes slugger Matt Kemp, acquired this month in a trade with the Los Angeles Dodgers. Kemp was the first of a few big deals by new Padres general manager A.J. Preller, who also has added outfielder Wil Myers, the 2013 American League Rookie of the Year, from Tampa Bay and All-Star catcher Derek Norris from Oakland.
San Diego has landed another of baseball's top power hitters in Upton, who is entering the final year of his contract and will earn $14.5 million. He had 29 homers and 102 RBIs last season.
Northcraft, 24, was a combined 7-10 with a 4.70 ERA at Double A and Triple A this past season.
The Braves have been rebuilding their roster after failing to make the playoffs last season, with an eye toward the opening of their new suburban stadium in 2017. The Padres are looking for an immediate payoff, having taken huge steps to pump up the majors' worst offense.
The trade for Upton came less than 24 hours after the Padres finalized a five-player trade with the Dodgers. The biggest name in the deal was Kemp, a two-time All-Star whose 182 homers rank fourth in Dodgers history.
San Diego also was finalizing an 11-player, three-team trade that will bring in Myers from the Rays. He would likely play center field, flanked by Upton and Kemp, to suddenly give the Padres one of the most dynamic outfields in the major leagues.
The Padres were also working on a deal Friday afternoon with the Red Sox to acquire third baseman Will Middlebrooks, a league source told ESPNBoston.com's Gordon Edes.
In addition, the Padres still have their three outfielders who got the bulk of the playing time in 2014: Cameron Maybin, Seth Smith and Will Venable. The best option for a deal would appear to be Smith, who hit .266 with 12 homers and 48 RBIs in 2014.
The trade of Upton had been expected since the Braves signed outfielder Nick Markakis to a four-year, $44 million deal. Atlanta had already dealt outfielder Jason Heyward to the Cardinals as the team clearly enters a rebuilding stage. Evan Gattis is expected to move from catcher to left field to replace Upton, though Gattis has been mentioned in trade talks.
Both Upton and Heyward were heading into the final year of their contracts.
ESPNLosAngeles.com's Mark Saxon and The Associated Press contributed to this report.