Todd Bodine, the defending series champion and last spring's winner at Atlanta Motor Speedway, followed Skinner past Bowyer to grab second place on lap 124 of the 130-lap event, but the leader was just too strong, pulling away to a five-length victory, the 21st of his truck career.
"I think the (No.) 30 (Bodine) was probably the better truck tonight, but I was a little better on short runs and the cautions just kept coming out," said Skinner, who drives a Toyota Tundra. "I was fortunate to get by Bowyer on that restart and was just able to hold Todd off for that last few laps."
The victory gave Skinner, who started the race tied with Jack Sprague for the series lead, the sole lead by 69 points over Bodine.
"Two races in a row we probably won with a second-place truck but, over the years, I've lost a lot of races with a first-place truck, so that's OK," said Skinner, who won two weeks ago at California Speedway after a dominating Mark Martin was knocked out of the lead on a restart by Ron Hornaday Jr.
Friday night's race was marred by a track-record nine caution flags, breaking the truck mark of seven set last fall.
After losing the lead, Bowyer slipped all the way to seventh before rallying to finish fifth behind Matt Crafton and Rick Crawford.
"Skinner just did what he had to do on that restart," Bowyer said, smiling. "It was probably payback. I did what I had to do to win in a race last year (at Texas)."
Bodine was disappointed by the finish.
"Our truck was just incredible on the long runs. But I knew when we got by Bowyer that there was no chance I was going to get (Skinner)," he said. "I saw earlier in the race that I was behind him for about 15 laps before my car came in and I could get by him.
"Our trucks were definitely equal on the short runs and mine was better on the long runs. I hated to see all those cautions at the end. We just didn't get the long run we needed. But our Tundra was pretty good and we'll take it."
Skinner, who started from the pole, and Bodine dominated the race, but Bowyer, a Nextel Cup regular and occasional truck racer, found himself just behind rookie and former open-wheel star A.J. Allmendinger after some late pit stops by the leaders.
After a restart on lap 97, Bowyer chased down Allmendinger and passed him for the lead on the next lap. Meanwhile, Skinner and Bodine, who restarted fifth and sixth, were charging toward the front.
Skinner passed Bowyer for the lead on lap 100, but another caution came out on lap 101 when Kraig Kinser crashed. Bowyer then passed Skinner on the restart on lap 109, taking Crawford with him.
Bowyer remained out front as two more caution flags waved for crashes by Bill Lester and Allmendinger. But Skinner got back out front for good, nudging Bowyer's rear bumper on the restart on lap 124 and taking advantage of the leader's slight wiggle to drive past on the outside.