After just missing a 17-foot birdie putt to win on the first hole, the PGA Tour rookie from Jupiter lost on the next hole when his tee shot on the par-three 17th at the Champion course at PGA National Resort & Spa found the water short of the green.
Berger ended up with a double bogey, which allowed Harrington to two-putt for par and the victory.
It was the second Honda title for Harrington, 43, of Dublin, Ireland, and his first PGA Tour win since the PGA Championship in 2008.
"Obviously a lot of things are being said about what this means going forward," said Harrington, a three-time major winner who now gets to play in the Masters next month. "The one thing you learn is you don't win as often as you think. I'm just enjoying winning the Honda Classic. When you win, make sure you enjoy it."
For Berger, 21, who played the Web.com Tour last year and has three top-10s in his last four events, the best finish of his young career was bittersweet.
"If you told me I was going to finish solo second when the week started, I'd probably take it," Berger said. "Right now, I'm not as happy as I wish I was. But it's a good learning experience."
Harrington hit his tee shot on the second playoff hole to within four feet, the best shot of the day on the 179-yard 17th.
"I said, 'You know, I'm first up on the tee, I've got to take control of this. I've got to hit the shot.' I knew I couldn't afford to bail out," said Harrington, who won a three-man playoff for his first PGA Tour victory at the 2005 Honda.
After that, Berger said he had to fire at the pin.
"That shot on 17 was kind of a dagger in the heart. I had to put it closer," said Berger, who hit the shot a touch heavy. "I knew right away it was wet."
Harrington won $1.098 million. Berger earned $658,800.
Berger was at 274 for the tournament on rounds of 68-71-71-64. Harrington, the second-round leader, shot 67-66-71-70.
Because of two rain delays Friday and a severe storm that ended play Saturday, the third round didn't conclude until early Sunday afternoon, then the players went right back out again.
Berger began the final round nine shots behind Poulter. He birdied three of his first four holes and was four under through 11 holes when play was suspended because of darkness at 6:18 p.m.
The 71 players resumed play at 8 a.m. Monday. Berger had five straight pars before birdies at 17 and 18 to get to six under.
Harrington had struggled on Sunday afternoon, going three over through seven holes when play was stopped. He said that was a big advantage for him.
"Things were not going well for me," Harrington said. "And I knew coming back out today that I was the challenger. It's hard to be the leader on this golf course, just like it's hard to be the leader at a major. So there is a little bit more patience on a tough course."
Sure enough, Harrington was the leader at seven under after the 14th hole. He birdied four straight holes while Poulter dropped five shots.
Poulter, who was eight under at the turn and led Harrington by five, doubled the 11th after hitting his approach in the water and tripled the 14th after hitting two balls in the water. He had also hit balls in the water on the fifth and sixth holes Sunday afternoon.
"Every time I went to hit a soft shot, I've got a chance of pushing it," Poulter said. "I hit a soft seven-iron into 11, made double. I hit a soft drive at 14. Three soft shots have gotten me into a lot of trouble this week. Making triples and doubles doesn't get it done."
Harrington had his own water troubles, dunking his tee shot at 17 and making double-bogey to drop to five under. Berger was watching the telecast in the clubhouse when he saw that he'd taken the lead.
Harrington bounced back on the par-five 18th, reaching the green in three, then rolling in a 15-foot birdie putt to pull even with Berger and set up a playoff starting on 18.
"I was quite afraid going to that 18th hole against him," Harrington said. "I knew he had a distance advantage on me.
"Thankfully I got away with that 18th. Daniel looked like he hit a good putt. I definitely felt like I got a second chance coming to the 17th."