The three-times Major winner shot a five-under-par 22 on the picturesque course, and was originally handed the title on his own when a thunderstorm hit Augusta and forced play to be abandoned.
Webb Simpson and Jonathan Byrd were both still out on the course at four under par with a chance to catch Harrington when play was abandoned. Byrd, however, had played to the final green and had a two foot birdie putt, which organisers later allowed him to hole to share the trophy with the Irishman.
It is a record third victory in the par-3 contest for Harrington following his wins in 2003 - when he shared the title with David Toms, again after weather prevented a play-off - and 2004.
It will also give Harrington another chance to break the jinx that has stopped the par-3 contest winner from ever going on to win the main tournament. The closest anybody has ever got since the first par-3 tournament in 1960 was Raymond Floyd, who led for most of the 1990 Masters before losing in a play-off to Nick Faldo.
Mark Wilson and Denmark's Thomas Bjorn both delighted the galleries with holes in one, at the fourth and ninth holes respectively.
Bad weather had already affected the build-up to the opening Major of the year, with an overnight storm on Tuesday forcing organisers to delay spectator entry to Augusta National as course staff cleared up debris for the final day of practice rounds at the Masters.
The Augusta area was hit with thunder, lightning, heavy rain and hail overnight while gusty winds sent twigs and pine needles on to the course.
"We lost several trees around the golf course, none of which were significant in the context that they will impact the competition," said Augusta National chairman Billy Payne.
"Debris was all around; took hours and hours, and the cleanup remains ongoing."
Spectators were allowed into the course Wednesday after a 40-minute delay.
"We had 1.4 inches of rain on the course. We have currently extremely wet conditions. We had our restroom at number 16 tee struck by a falling tree, significant damage. We hope to have it rebuilt and up and running by the end of the day," said Payne.
"Several of our bunkers were completely washed out. We expect them to be fully restored to competitive conditions by the end of the day."
Tiger Woods, the bookmakers' favourite for the title, had to walk through some of the debris during his practice session.
The weather forecast for Thursday's opening round predicts a 70 percent chance of rain with thunderstorms likely, especially in the afternoon and evening.
With some players, including Woods, complaining about muddy balls and wet conditions likely for some of the April 5-8 event, the organisers have the option of allowing players to 'lift, clean and place' their ball.
But Payne said Augusta National would be reluctant to go down that path.
"We surely would not want to have to do that. That would be a decision very difficult to make," said Payne. "However, we are also bright enough to know that weather conditions can have an impact on that, and possibly cause us to change our minds on that issue."