Fourteen players were still out on the course when play was suspended in fading light on Thursday, South African Tyrone van Aswegen the best placed at four under with two holes to play.
However, van Aswegen was unable to get any closer to the superb eight-under 63 fired by Villegas as he finished par-bogey for an opening 68.
That left four-times PGA Tour winner Villegas three ahead of Americans Bubba Watson, Chez Reavie and Luke List, who all completed their 66s on Thursday.
"I was a little surprised with my eight-under to be honest," said Villegas, who had missed the cut in his previous four events. "This is a golf course where it's not easy to shoot eight-under.
"I was surprised with some of the putts I made, because the greens are not greens where you're expecting to make 20-footers and just kind of bumping in the hole. It's a crazy game."
World number three Rory McIlroy, making his first PGA Tour start of the year, was a further stroke back with six other players after opening with a 67, while top-ranked Jordan Spieth was a staggering 16 shots off the pace after carding a 79.
It was Spieth's worst opening round ever on the PGA Tour.
(Editing by Larry Fine)
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