The 30-year-old right-hander was the team's opening day pitcher last season, giving up six runs in four innings, then did not take the mound again the rest of the year, eventually undergoing surgery on his pitching shoulder on Aug. 4.
Arizona would have had to pay a $2 million buyout if it had declined the option.
"He's worked very hard since the surgery," general manager Josh Byrnes said, "and we're confident that he'll return to be a very healthy, effective pitcher."
A three-time All-Star, Webb won the 2006 NL Cy Young Award and was second in voting the next two years. He is 87-62 with a 3.27 ERA in seven seasons. He ranks second in franchise history to Randy Johnson in wins, starts (198), innings pitched (1,319 2-3) and strikeouts (1,065).
Webb's 15 complete games rank behind Johnson and Curt Schilling for the Diamondbacks.
Byrnes and Webb spoke on a conference call shortly after the announcement was made.
Webb said he knew that the Diamondbacks picking up the option "was up in the air I think for awhile and rightfully so."
The successful surgery and subsequent good reports on rehabilitation had made it probable that the team would pick up the option.
"We did want to use the time we had but once we got out of the surgery all signs had been positive," Byrnes said.
Asked about the risk of the move, Byrnes said, "There's a risk in everything."
"I think there's a lot of reward," he added. "You're talking about one of the best pitchers in baseball."
Webb plans to throw for the first time since the surgery next Wednesday, some soft tosses before shutting down and beginning his normal buildup to spring training.
He's confident that he will still have the nasty sinker that made him one of the league's best pitchers.
"Even when I was throwing and I was still having some pain, the life on the ball was still there," Webb said. "I can't be too sure, but I'll probably always have that sinking action."
Webb had pitched more than 200 innings each season from 2004 through 2008 and won 56 games from 2006 through 2008. He went 22-7 in 2008, tying Cleveland's Cliff Lee for the most victories in the majors.
Before last season, Webb had only been on the disabled list once as a major leaguer, missing 15 days with right elbow tendinitis in 2003.
"It's been tough," he said. "I'm usually used to being out there as much as anybody. It's tough to sit on the sideline and see the team struggle."
Webb tried to work his way back from the injury without surgery but after getting opinions from three doctors outside the Diamondbacks organization, he decided to go ahead with the operation.
Texas Rangers physician Dr. Keith Meister performed the surgery.
Webb thought he had a three-year contract extension with Arizona in 2008 but the club withdrew the offer, citing insurance company concerns regarding the shoulder. Webb disputed the findings, then came the shoulder problems this year and any new deal became out of the question.
His future with Arizona beyond next season is uncertain.
"Obviously it's going to depend on how the season goes for me as well as for the team," Webb said. "Hopefully it goes well for both of us and we can maybe start some talks toward the end of the season next year."