Two holes later, came another bogey when he failed to get up and down from short of the green at the par-3 14th.
McIlroy had been four over par after two holes of his second round and despite a flawless 65 on Saturday, started the final day five shots off the lead shared by Kisner and Hoffman.
Northern Irishman Rory McIlroy (69) three-putted the last to finish two strokes behind.
Kiwi golfer Danny Lee climbed 39 places in the final round of the Arnold Palmer Invitational at Bay Hill in Florida on Monday (NZ time) to finish in a six-way tie for 17th.
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The world number three birdied the par-5 12th, sank a 30-foot eagle putt at the par-5 16th, then sent his tee shot at the par-3 16th into the water on the way to a double bogey.
Leishman, who finished 11-under overall, clinched his second career PGA Tour victory with a strong finish. "I remembered I'd missed that putt left so I backed off, adjusted my read about 2 feet and made it. Practice pays off". It's unbelievable. Obviously, it's sad not to have him up there on 18, but to play how I did and to win any tournament's huge, but especially this one. Leishman never looked back, closing with a three-under 69 to win by one.
The two leaders still have plenty of work to do Sunday as a handful of players are just a few strokes behind them.
"I'm really pleased with how I went this weekend and can take a lot of positives from it", he said. I gave myself chances for putts and, yeah, it was an awesome day and I couldn't have drawn it up any better. Hatton finished tied fourth with McIlroy while Fleetwood's final-round 68 put him tied for 10th and will firmly secure his spot at his first ever Masters.
He commented: "It's always hard, but we all try to peak for the first week in April at Augusta, and I certainly seem to be trending in the right direction at the moment". He recalled this week that the two spent a couple hours in Palmer's office at Bay Hill, had lunch and then played nine holes together in the afternoon.
But each time McIlroy posted a birdie he seemed to curb his momentum with bogeys at the third, seventh and holes before the disappointment on the 72nd green.
"These things happen", McIlroy said. It was good to throw in one of the few bogey-free rounds on day one, and I kept it going well in tough conditions this time. He has easily been the most improved player so far this season. I've been trying extra hard for him and it was great today that he was here and a special day with everything honouring Mr Palmer.