The 40-year-old Dubliner became the first player to win a hat-trick of par three titles, although just like his first victory in 2003 he had to share the honour.
The fun event could not be completed because of a thunderstorm, leaving Harrington as joint winner with American Jonathan Byrd after both returned five-under-par scores of 22.
Since the par three event started in 1960, nobody has lifted that crown and then won the event proper as well four days later.
In 2003 Harrington tied with David Toms, but bad weather prevented a play-off then as well. Twelve months later he beat Argentina's Eduardo Romero in sudden death.
Last year's Wednesday champion Luke Donald did not even take part this time because he wanted to focus on the main event, while Open champion Darren Clarke was another non-participant because he wanted to rest a sore groin.
Most players treat it as light relief and invite family, friends or even celebrities to act as their caddies.
Lee Westwood and Thomas Bjorn had television presenters Ant and Dec - Anthony McPartlin and Declan Donnelly - carrying their bags, Bjorn finishing with a hole-in-one.
Harrington went round with his sons Patrick (eight) and Ciaran (four), as well as Japan's Ryo Ishikawa and American amateur Patrick Cantlay.
"This is my 13th time playing it and the least amount of wind, so the scoring was on," he said. "The whole thing is memorable. I didn't hit anything stone dead or anything like that."
He actually missed the last green and was close to going into the water, but chipped to four feet and saved par.
Former US Open champion Jerry Pate, winner of the par three in 2005, might have denied Harrington, but could not continue after reaching four under after five holes.
Winning again would not have bothered Pate as he is not playing in the actual Masters.
The par three is open to many major champions whose days of participating in The Masters are over.
Television commentators Sir Nick Faldo, Johnny Miller and Ian Baker-Finch also took part, as did Arnold Palmer, Jack Nicklaus and Gary Player.
That illustrious trio had another function to carry out, hitting ceremonial drives off the first tee in their roles as honorary starters.