Paulino, the Astros' No. 6-ranked prospect by MLBPipeline.com, was suspended 80 games without pay on July 1. for testing positive for Boldenone, a performance-enhancing substance, in violation of Major League Baseball's Joint Drug Prevention and Treatment Program.
Paulino is expected to be ready for Spring Training.
"It was an awkward timeline for him not being healthy and having one day left in the season [that] he was going to be eligible," Astros manager A.J. Hinch said. "He'll rehab over the winter."
The 23-year-old Paulino, who made his Major League debut last year, was 2-0 with a 6.