At the closing hole at the TPC at Sawgrass, Scott, who had a two-shot lead, found the fairway off the tee. He pulled his second into the water and suddenly the possibility of a playoff loomed.
But Scott, who got a short game lesson from mentor Greg Norman earlier in the week, chipped to 10 feet. He needed to hole the putt to avoid sudden death with Harrington and that's what he did to become the youngest winner of this event at the age of 23.
'I felt good and everything. It's just one of those things that always seems to happen around this place,' said Scott, who pocketed $1,440,000 for the victory. 'I was glad I had a putt to win. I've had a few in the past and not made them. I felt it was my turn.'
Scott posted a 2-under 70 on Sunday to finish the championship at 12-under-par 276.
Harrington used a back-nine 30 to shoot a 6-under 66 in the final round. He finished at 11-under-par 277 as he has yet to reach the winner's circle in a PGA Tour event.
'It was a little disappointing, but I'm happy with my own personal performance, so what can I say,' Harrington said. 'I didn't really think there was going to be a playoff until obviously his errant second shot on 18.'
Phil Mickelson (71), Kenny Perry (71) and Frank Lickliter (72) shared third place at 8-under-par 280.
Tiger Woods never mounted a charge on Sunday. He only managed a 1-over 73 and shared 16th place at minus-3.
'My swing is good if I let it go and trust it, but when I get out there and I see a little trouble and I've got a little wind and have to hit a shot in play, I don't trust it,' said Woods. 'I didn't quite hit it good enough.'
Scott opened the final round with a two-shot lead and extended it to four thanks to four birdies and a bogey through his first eight holes.
Things went downhill for the young Australian on the back nine. He nearly landed on a cart path off the tee at 10 but missed the green with his second. Scott's chip left him with 12 feet for par and the putt didn't fall so Scott's margin was cut to three.
Scott wasted little time in rebounding with a short birdie putt at the 11th and an eight-footer at the 12th. He was once again four ahead of the field but Sawgrass and some poor decisions nearly cost Scott the title.
Scott elected to hit driver off the tee at 14 and his drive landed in the right rough. By the time he got to the green, Scott had 20 feet for par and he missed the putt.
As Scott bogeyed the 14th, Harrington was three-under on his round and climbing up the leaderboard. Harrington landed a five-iron three feet from the hole at the par-five 16th and converted the eagle putt to get within three of Scott's lead.
Harrington knocked a seven-iron to 12 feet at the last and ran home the birdie putt. He headed to the range in the chance that Scott would squander his two- shot edge.
Scott nearly cemented the victory at the 16th. He missed the green with his second shot but chipped to three feet. Scott's birdie try did not fall and now it was on to the famous 17th.
Scott made a routine par at 17, as routine as you get on the island green. He found the fairway at 18 and the engraver was already etching Scott's name on the trophy.
But thanks to a solid chip and some advice from Norman, Scott joined Steve Elkington and Norman as the only Australians to win the Players Championship.
'I probably would have lost the tournament, to be honest with you, if I was chipping the same way as I did earlier in the week,' said Scott, who won his second PGA Tour event after last year's Deutsche Bank Championship. 'Joining Greg and Steve obviously is huge, but the list is long here. It takes something to win this tournament.'
Fifty-year-old Jay Haas matched Harrington with a 66 on Sunday. Haas tied for sixth with Jerry Kelly (72) and Kevin Sutherland (73) at seven-under-par 281.
Reigning PGA Champion Shaun Micheel fired a five-under 67 to finish alone in ninth at minus-six, followed by Fred Funk (71), Paul Casey (72) and Bob Burns (72), who were knotted at five-under-par 283.
John Daly shot an 80 on Sunday but still received some great news. While Scott passed him on the money list, Daly remained in 10th place and that was good enough for an invitation to the Masters in two weeks.
Any player who was not already eligible and finished in the top-10 on the 2004 money list after this event, is entered at Augusta National in two weeks.