The 49-year-old Armour, a two-time PGA Tour winner, began the day with a five-stroke lead over Rich Beem. But Armour finished regulation with a 4-over 76 in a round that included four bogeys, a double bogey and two birdies.
Simpson, a former U.S. Open champion, finished with a 70 after beginning the final round trailing Armour by six shots.
MacKenzie, a former Nationwide Tour player without tour status for 2009, rallied from a nine-shot deficit with a final-round 67.
"I hit some shots that were close to being really good," said Armour, who earned $60,000 of the $300,000 purse. "They just didn't turn out to be that good. But that's part of the inner battle of winning a golf tournament."
The 37th annual event featured players from the four major tours. Champions Tour and women pros received tee shot advantages.
Armour, the first repeat winner in the tournament's 37-year history, ended a four-year winless streak with his Callaway victory in 2007. He last won on the PGA Tour at the Valero Texas Open in 2003, when he set the PGA Tour tournament record of 34 under par.
"When the wind picks up at Pebble Beach it's a challenge," Armour said. "It wasn't easy, but then again, winning a golf tournament is never easy."
Armour and Simpson, playing in the same foursome, were tied at 11 under after 15 holes. Simpson bogeyed the 16th and 17th holes to fall one shot behind Armour and MacKenzie, who had already finished.
Simpson made a 12-foot birdie on the 18th hole to slip to 10 under. Armour missed a 24-foot birdie attempt for the win but made a 4-foot par putt to join the three-way playoff.
"I just wanted a good finish," said MacKenzie, a member of the 2003 Walker Cup team. "I started off really good. I saw that third place was about three shots away and all I wanted then was a good finish."
Vicky Hurst, who will be a rookie on the LPGA Tour in 2009, shot a final-round 73 and led the three women who advanced to the final round at even par.
Tom Purtzer of the Champions Tour had a final-round 67 and finished alone at 9-under.
Second-year PGA Tour pro Nicholas Thompson (71), 2006 AT&T Pebble Beach National Pro-Am winner Arron Oberholser (73), and former PGA Championship winner Beem (73) finished at 280.