He was 0-for-1 with a walk before giving way to Jerry Hairston Jr.
Cora committed an error in the second inning, when he could not handle a Carlos Ruiz ground ball that led to Philadelphia's only run in a 2-1 Washington win.
"Alex was really under the weather," said manager Jim Riggleman. "If Alex Cora doesn't catch a ball then it doesn't get caught -- he's that good over there."
Cora also had a collision with Phillies slugger Ryan Howard in the second inning, when Cora went to apply the tag to Howard on his slide into second on a double. Howard's helmet hit Cora in the neck, and Cora appeared shaken up though he remained in the game until exiting two innings later.
Hairston had an injury scare of his own in the fifth, when he raced Wilson Valdez to third base for a force out. Hairston stepped on the bag as Valdez slid into it, and their feet tangled up, sending Hairston to the ground. Hairston remained in the game.