Pena was pulled off the bag trying to catch shortstop Starlin Castro's throw on Justin Upton's grounder. The throw was wild and Castro was charged with an error.
Cubs manager Mike Quade said Pena wanted to stay in the game and hit in the eighth, but they opted to use pinch-hitter Reed Johnson. Pena is hitting .200 in four games and contributed a sacrifice fly Monday in the Cubs' 4-1 win over the D-backs.
If Pena can't go Tuesday, the Cubs could use either Jeff Baker or Tyler Colvin at first.