The Nationals, losers of nine games in a row entering Sunday, optioned catcher Jesus Flores to Triple-A Columbus.
Washington cut short Pena's rehab assignment at Columbus after only one game, an 0-for-2 showing Saturday. He was in Washington's starting lineup Sunday, playing left field and batting fifth.
Pena injured a side muscle during spring training.
Flores hit .364 (4-for-11) with two doubles, a homer and three RBIs in four games this season. He originally was slated to spend this season in the minors but made Washington's Opening Day roster because of an injury to top reserve catcher Johnny Estrada.