"It's probably good for him just to take a breather and coming back up here and learning something more, sometimes that can be overkill for a young player," D-backs general manager Kevin Towers said.
Bauer, the No. 3 overall pick, signed quicker than most first-round picks and quickly moved up from Class A Visalia to Double-A Mobile, where he pitched well in his first three starts before struggling in his next two.
In his final start of the year on Sunday, Bauer was the winning pitcher as the BayBears captured the Southern League title.
The 20-year-old is expected to contend for a spot in the rotation next year at Spring Training.
"I think he finished on a strong note, which is good," Towers said. "He's been through a lot. He's going to be in the mix to be one of our pitchers next year, so I think the rest and getting mentally prepared and physically prepared will be a good thing."