Flanagan, the 2003 U.S. Amateur champion, birdied the third extra hole to defeat Chris Baryla for the title. Roland Thatcher and Bryn Parry had been eliminated on the first two extra holes.
Flanagan carded a 2-under 70 in the final round to finish at 13-under-par 275. Baryla, Parry's playing partner, matched that 70, while the final pairing of Parry and Thatcher each carded final-round 71s to force the extra session.
Back at the 18th for the third playoff hole, Baryla found a greenside bunker with this second shot. Flanagan's second bounced just over the green into the rough.
Baryla blasted out to 4 feet, then Flanagan chipped within a foot. Baryla's birdie putt never touched the hole as he pulled it left. He tapped in for par then stepped aside as Flanagan tapped in for birdie and his first tour title.
'That's about the longest half-foot putt I've ever had,' joked Flanagan, who picked up $81,000 for the win. 'I hit the ball well all week, didn't putt too great, but got away with it. I'm very, very happy.'
At the 18th in regulation, Thatcher had the best chance to win, but two-putted for par from 18 feet out. The other three all got up and down for par to head into the playoff at The Dominion Club.
Parry was the lone player to miss the fairway off the tee at the 18th, the first playoff hole. He laid up, then knocked his third to about 50 feet. The other three players all found the short grass of the tee and putting surface with their second shots to the par-5.
Baryla played his third after Parry and Thatcher. Baryla knocked his eagle effort within a foot and tapped in for birdie to eliminate Parry, who left himself 7 feet for par. Thatcher and Flanagan safely two-putted for birdie to extend the playoff.
'I'm disappointed I didn't have a go at it there at 18,' admitted Parry. 'The lie was iffy and seeing how this turned out I wish I had a go at it.'
At the par-3 ninth, Thatcher left himself over 50 feet for birdie before Flanagan pulled his tee ball into the left rough and Baryla knocked his tee ball to 45 feet.
Thatcher hit a poor first putt leaving himself 10 feet for par and he missed that to drop out of the playoff. Flanagan pitched within a foot and tapped in for par, while Baryla two-putted for his par.
Then the former U.S. Amateur champion hoisted the trophy.
The playoff could have been even bigger as Chris Smith (68), Greg Chalmers (69) and Brad Elder (70) shared fifth place at 12-under-par 276.
Flanagan had an up-and-down front nine, where he carded four birdies and three bogeys. He birdied 14 and 15 to grab the lead at 14-under, but bogeyed 16 to get in at 13 under.
Baryla posted three birdies and a bogey on the front nine to turn in 13 under. The Canadian birdied 12, but gave that shot back at 13. Baryla bogeyed 15, but rebounded with a birdie at 16 to join Flanagan in the house at minus-13.
Parry birdied the second, as did Thatcher, to remain tied for the lead at 13 under. Parry flew out in front with three straight birdies from the fourth to pull four strokes clear of the field.
However, Parry three-putted for bogey at seven. He got that stroke back with a birdie on nine, but bogeyed the next and found more trouble at 11. Parry's tee shot came up short in the water. He hit the green with his third, but two-putted for double-bogey. Parry parred the final seven holes to gain entry into the playoff.
'I did hit a good shot there,' said Parry of his approach at 11. 'I guess I was hitting it so good I was hedging my bets that I could hit it close and I probably didn't need to. I hit a good shot and I'm going to have to live with that.'
Thatcher faltered to a bogey on seven to slide back to 12 under. He grabbed a piece of the lead with a birdie on 12, but fell one back as he bogeyed 15. Thatcher regained a piece of the lead and eventually a spot in the playoff thanks to a 25-foot birdie putt at 16.
Nicholas Thompson, winner at the HSBC New Zealand PGA Championship, and Livermore Valley Wine Championship winner Omar Uresti ended in a tie for eighth at 10-under-par 278. They were joined there by Rick Price and David Sanchez. Five more players were one stroke further back at minus-9.