Pena hit .363 with 52 runs, 17 doubles, 21 home runs and 63 RBIs in 63 games with Reno this season. Before joining the D-backs, he led the Pacific Coast League in home runs and slugging percentage (.726), and was tied for first in RBIs.
The 30-year-old Burroughs, returning to the big leagues for the first time since 2006, hit .250 (6-for-24) with a run and a double in 23 games for Arizona.
Pena -- who has also spent time with the Red Sox, Nationals and Reds in parts of seven seasons of service -- is a career .253 big league hitter with 196 runs, 67 doubles, 77 homers and 225 RBIs in 560 games.
The 29-year-old Pena last appeared in the Majors with the Nationals in 2008, and signed with the D-backs as a Minor League free agent on Dec. 9, 2010.
Arizona is in action Tuesday night against the Royals in Kansas City.