Both players had parred the first extra hole, also the 18th, with Dufner sinking a clutch 10-footer to keep his title hopes alive after he had conjured a miraculous escape on the penultimate hole of regulation, the par-three 17th.
Dufner, who won his fourth Tour title, came perilously close to finding water off the tee on 17. However, his ball ended up in a clean lie beside rocks just off the back of the green from where he nearly holed out for birdie before tapping in for par.
"I thought I was in the water," the 38-year-old told Golf Channel about his wayward tee shot. "I got a great break. Sometimes those things happen, you need those to happen to win after you hit a poor shot.
"I looked at it and had a pretty clean lie ... I leaned the shaft a little bit with the face open and tried to hit one where you kind of get a lot of grip. I thought it was going to sneak in there for a minute.
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"I am fortunate to be in this position and happy to be playing good golf again," added Dufner after ending a title drought dating back to his victory at the 2013 PGA Championship.
For Lingmerth, who secured his first PGA Tour win at last year's Memorial Tournament, it all came down to a "little mistake" with his approach from the right rough on the second extra hole.
"I didn't choke up enough on the club," said the 28-year-old. "The grass just grabbed it a little bit, which made the ball turn over. It wasn't really a bad swing, just a little mistake on my part."
The duo had finished the 72 regulation holes at 25-under 263 after a wildly fluctuating final round where four players held at least a share of the lead.
Dufner narrowly missed a 20-foot birdie putt at the last before carding a two-under 70 while Lingmerth carded a bogey-free 65 at PGA West's TPC Stadium Course.
Twice former champion Phil Mickelson, competing in his first event since last October's Presidents Cup, closed with a 68 to share third place at 21 under with fellow Americans Andrew Loupe (68) and Kevin Na (68).
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Andrew Both)
