The left-hander outlasted world number three and defending champion Adam Scott through seven nervy play-off holes at Royal Pine.
It marked Chalmers' second PGA Championship win, having lifted the trophy in 2011.
Chalmers carded a final-round eight-under 64 to finish tied with Scott (71) and Wade Ormsby (71) at 11 under.
Scott and Chalmers birdied the third play-off hole, eliminating Ormsby after he could only manage a par.
Ormsby had missed a putt to clinch the title on the second play-off hole.
Scott looked the more likely winner before his putter let him down, bogeying the seventh play-off hole to allow Chalmers to tap in for victory.
New Zealand's Michael Hendry (71) finished fourth at nine under, a shot ahead of American Scott Stallings (70).
Boo Weekley (74) slipped to sixth, a stroke clear of Australians Matthew Giles (70) and Scott Strange (76).
Completing the top 10 were John Senden (69) and Cameron Smith (70) at five under.