The 25-year-old Canadian, who has led since his opening round 61, was three ahead of the field when he floundered in a fairway bunker on the par-four 11th.
Hughes, facing a nasty lie, failed to get out of the sand and came out weakly with his next shot. His approach left him some 60 feet from the cup and he three-putted for seven.
"I was like, `This hole is never going to end,'" the 25-year-old told reporters. "It finally did, and it worked out all right."
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Pan temporarily assumed the lead with a pair of birdies as Hughes triple-bogeyed, but dropped a shot with a bogey at 13 after a poor tee shot.
Villegas made a rousing finish on a breezy day with four birdies in a row for 64, finding himself in a four-way tie for the lead before Hughes' birdie at 16.
"It was playing a little tougher out there with the wind, but the putter got hot," said the Colombian, who overcame a double bogey at the third. "I made pretty much everything."
Horschel, who like Villegas attended the University of Florida, shot a bogey-free 65 and celebrated his round and a football win by the Gators with a leap of joy on the 18th green.
"I'm hitting the ball really good, the best I have in 18 months," said Horschel, who has not won since claiming the FedExCup title with a Tour Championship victory two years ago.
"I was able to control my golf shots," said Horschel, who could not contain himself after word of Florida's 16-10 win over Louisiana State University was relayed to him.
"Big win over LSU today," he said. "Nice to stick it to LSU fans."
(Writing by Larry Fine in New York; Editing by Peter Rutherford)
