The result was a two-way tie for the lead at 11-under 131 halfway through the Phoenix Open.
Wilson birdied the last four holes for a 5-under 66, while Villegas bogeyed No. 18 when he missed a 14-foot putt for par. The 28-year-old Colombian settled for a 69 after tying the tournament first-round record with a 9-under 62 on Thursday.
Eleven players were within two shots of the lead at TPC Scottsdale, where a crowd estimated at 101,709 attended the second round Friday under thinly overcast conditions.
Tom Lehman, nine days shy of his 51st birthday, had a 67 to top a group of six at 9-under. Play was suspended because of darkness with one player, Matt Every, still on the course. He had a three-footer for a birdie that would put him at 9-under.
Wilson, who said he was ill early in the week after returning from the Mayakoba Golf Classic in Cancun, Mexico, considers himself the bland one among those at the top of the leaderboard.
"I'm not a flashy player. ... I see Anthony and Rickie and Camilo up there and they're all very flamboyant characters, and it's fun to watch them," Wilson said. "So I'll be somewhat of a spectator too but certainly taking care of my own business."
Villegas, who mixed three bogeys with an eagle and three birdies, insisted he was satisfied with his second round.
"It's tough to shoot 9-under in one day. To do it two days in a row, it's even harder, obviously," he said. "Am I disappointed the fact I didn't go low-low today? No. You just want to stay in the tournament. I mean, after a great first day, you just want to keep plugging, keep staying there and give yourself a chance come Sunday afternoon."
Wilson said this is the kind of desert course, with the open par-5s and par-4s and friendly greens, where golfers can get on the kind of runs that he did late Friday.
"I made a lot of putts, so if you're seeing the lines good you can roll off a string of birdies pretty quick," he said.
As many as 150,000 fans are expected for Saturday, always the wildest day in the biggest party on the PGA Tour.
"I have fun," Villegas said. "It's one week a year where we get to experience this."
Tee times Saturday were moved ahead an hour because of the chance of rain late in the day. Rain is more likely Sunday.
After a bogey-free first round, Villegas made the turn Friday at 1-over for the day but regrouped with a birdie at No. 10 and an eagle on the 13th to regain the lead at 11-under. He moved to 12-under with a birdie on the 15th.
On the 18th, his tee shot cleared the lake but landed in a large bunker next to a bush. He punched his second shot onto the fairway, and then his third shot left him a 14-footer for par.
"We had a good shot at it," the 21-year-old Fowler said. "Hopefully we'll give ourselves a better one this year."
Englishman Ian Poulter, winner of Sunday's Match Play championship down the road in Marana, Ariz., followed a 1-over 72 on Thursday with an 8-under 63 on Friday. He felt so exhausted after last week's big win that he fully anticipated missing Friday's cut.
"I even booked a plane for takeoff at 3 this afternoon," Poulter said. "I wasn't feeling good. It's just nice to go out there and hit good golf shots, play well and put myself in a position now where I've put myself into form."
Phil Mickelson was within reach of the lead after consecutive 68s left him at 6-under.
Arizona State senior Braxton Marquez, who didn't travel with his Sun Devils golf teammates this week and earned a spot here in Monday's qualifier, shot a 65 to make the cut at 3-under 139.