The Childress cars took the top two spots, six days after the team swept the top three positions in the Sprint Cup series race at Bristol.
Wimmer edged Bowyer by 0.578 seconds for his sixth victory in 149 Nationwide Series starts and first since 2003. Carl Edwards was third, followed by Brad Keselowski and Kelly Bires. Bowyer took the series points lead from Kevin Harvick, the fellow Childress Sprint Cup driver who skipped the Nashville race.
"I felt like we let three or four races get away from us last year, including this one, so it was nice to get the job done today," Wimmer said.
Kyle Busch started on the pole and was the class of the field, leading a race-high 125 laps before spinning out with 62 laps left. The Sprint Cup points leader grazed Bowyer, who was passing on the inside, and was forced to pit for repairs. Busch finished 16th.
"It was just driver error," Busch said. "I just messed up and lost it. I'm sure it's going to bother me all week."
It was the first stand-alone Nationwide race of the year and Wimmer became the first non-Sprint Cup regular to win in the series.
"I've raced in the Sprint Cup Series but not a lot lately," Wimmer said. "Sitting down and running a partial Nationwide schedule is not what I want to be doing, but those are the cards that are dealt to me now and I'm with a great team.
"You can struggle with a single-car operation or a lower budget team and that's not where any driver wants to be. I'm just trying to do the best I can for Richard right now and hopefully sometime I'll get back to racing Nationwide or Sprint full-time."
The race extended a streak for Bowyer and ended one for Edwards. Bowyer finished second for the fourth consecutive time at Nashville, while Edwards' three-race winning streak on the 1.3-mile oval came to an end.