Johnson won the Crowne Plaza Invitational at Colonial by one shot over Dufner, finishing at 12 under par. The '07 Masters champion shot even-par 70 on Sunday.
Johnson incurred a two-stroke penalty on the final hole after moving his marker a putter-head but failing to move it back into its original spot after replacing it before he stroked his final putt.
Dufner made a triple-bogey seven at No. 15 after putting his approach in the water hazard. That left Dufner four behind with three to play.
The Auburn product also found the water at No. 9 en route to 4-over 74.
The win is the eighth on the PGA Tour for Johnson and the first since his win here in 2010.