Choo, who missed seven weeks earlier this season with broken thumb, was a late scratch from the lineup. Shelley Duncan took Choo's place in the lineup.
The slugging outfielder homered twice Tuesday, despite nearly missing the first game of the doubleheader to be with his wife and newborn daughter.
On the season, Choo is batting just .262 with eight home runs and 36 runs batted in. He hit at least .300 in the previous three seasons and clubbed 22 home runs during the 2010 campaign.