In 2012, Johnson won the Crowne Plaza Invitational at Colonial for the second time in his career. He made a five-foot putt on the last hole for what appeared to be a three shot victory, but a ruling on the final hole resulted in a two-stroke penalty. It did not affect the outcome of the tournament, with the only difference being Johnson signing for a 6 instead of a 4 on the final hole, with Johnson winning by a single stroke over Jason Dufner. He jumped to 3rd in the FedEx Cup standings and returned to the world top 20 with this victory.
Johnson moved to second in the FedEx Cup standings with a playoff win on July 15, 2012, at the John Deere Classic. Johnson defeated Troy Matteson, who started the day up four shots on Johnson and had led the tournament since the first round, with a birdie on the second hole of their playoff. Johnson also started the day behind three-time defending champion Steve Stricker, who was three shots behind Matteson. It was Johnson's second win on the year after winning at Colonial Country Club. Mike Bender, Johnson's swing coach, also caddied for the week while usual caddie Damon Green played in the U.S. Senior Open.
At the 2012 Open Championship, played at Royal Lytham & St Annes Golf Club in Lancashire, England, Johnson finished at even par for the tournament (280), tied for ninth, seven shots behind winner Ernie Els.