Harrington returned to PGA National early on Saturday to complete his second round following frequent weather delays over the first two days, and he added a 66 to his opening 67 to hit the front on seven under par – one shot clear of American Ryder Cup star Patrick Reed.
But the 43-year-old was unable to begin his third round, and only eight groups were on the course when officials suspended play yet again due to approaching thunder and lightning.
Heavy rain then rendered the course unplayable, and the decision was taken to abandon play for the day with the third round action set to resume on Sunday at midday (GMT). Tournament organisers remain hopeful of completing 72 holes by Sunday evening, with the weather forecast looking brighter for the final day.
A two-tee start has been enforced with players going out in threeballs, and Harrington will be last out alongside Reed and Ian Poulter, who continued his encouraging recent form as he moved within two of the lead after a superb 64, equalling the best round of the tournament.
Harrington had just birdied the 16th on Friday before play was suspended due to darkness, and he resumed on the third morning with birdies at 17 and the first hole before getting into bother at the long third and running up a bogey-six.
But the three-time major champion, who has slumped to 297th in the world rankings, responded with three consecutive birdies, although he undid much of his excellent work with a bogey-bogey finish at eight and nine.
“Obviously I want to be at the top of the leaderboard and I want to be trying to win tournaments. Five tournaments ago, I won, so it’s not like it’s an alien feeling for me,” said Harrington.
“I think I’m in a good place that I can deliver more performances like this. So I’m not panicked about going out and it all having to happen this weekend.
“At times I get lost and distracted from the process. Ultimately that’s what has changed. I had it going out there for a while. I was struggling with it the last couple of holes.”
Reed reeled off five birdies in a second-straight 67, while Poulter vaulted into a share of third place with Brendan Steele after a sparkling round featuring an eagle, five birdies and just one dropped shot at the 15th.
“It was always going to be tricky,” Poulter said of the blustery conditions. “The round started to pick up. I putted nicely. I played a pretty steady round.”
Luke Donald is three off the lead after a solid 67, while Scotland’s Russell Knox is well-placed on three under after a 68 and Phil Mickelson comfortably made his first halfway cut of the year at the third attempt after completing a 67 in atrocious conditions to move to two under.
After the cut was confirmed at four over, Justin Rose and Graeme McDowell will have the weekend off along with world No 1 Rory McIlroy, while star South African trio Ernie Els, Charl Schwartzel and Retief Goosen also crashed out.