John Rollins was one shot behind after 64.
It was also a good day for former Augusta Prep golfer Courtland Lowe.
Lowe, who graduated from Augusta Prep in 1998 and went on to play at Wake Forest, easily made the cut in his first PGA Tour start.
Lowe, who made the field through a Monday qualifier, has shot 71-72--143. The cut came at 146. Lowe opened with his 71 on the easier North Course and shot 72 on the South Course.
Also at 146 is Augusta native Charles Howell, who has shot 72-71 after playing the South Course in the first round and the North Course in the second round.
Villegas teed off in a steady rain, and when he reached the exposed holes along the Pacific bluffs, more rain arrived equipped with gusts up to 25 mph that made the San Diego weather feel more like Sun Valley. But he scrambled for pars, took advantage of a few par 5s and wound up with a 2-under score that put him at 11-under 133.
"I looked at my caddie walking down the 10th fairway -- it was just pouring -- and I told him, 'Listen, let's find a way to keep it around par and maybe get it in the red numbers,' " Villegas said. "I scrambled pretty good and 2-under, I'm happy with it."
Villegas was among the early starters, and his solid round made it look as if this Buick Invitational might turn into a runaway. That changed when Rollins played the front nine (he started on No. 10) in 31.
"When I saw he was at 11 (under), I was just trying to get in position to be in the last couple of groups, just staying in the mix," Rollins said. "It just so happened things started going in."
He caught Villegas at 11-under with a birdie on the par-3 eighth and had a chance to match the South Course record since 2002 -- when Rees Jones first began to lengthen the course for the U.S. Open -- until a bogey on the par-5 ninth.
Charley Hoffman, who grew up in San Diego and is coming off a playoff loss last week at the FBR Open, shot 66 on the easier North Course and was at 7-under 137. The group at 138 included Paul Goydos, who wasn't planning to play the Buick Invitational.
Goydos learned two weeks ago that his ex-wife had died, and he said he would take a break from the PGA Tour to be with his two daughters, for whom he had full custody. He said he did not want to talk about his family yet, preferring to answer questions only about his golf and his chances on the weekend.
"I'm not overly excited about playing long ball with Camilo on the South Course the next two days. There's really not much advantage for me there," Goydos said. "But I'm just happy to be playing well, and happy to be playing on the weekend."
Phil Mickelson, coming off a missed cut at the FBR Open, also is playing the weekend, although not as close to the lead as he would like.
He made three bogeys on the par 5s at the North Course for 72, leaving him at 2-under 142.