Giambi has been suffering from an intestinal parasite condition that his personal trainer said could keep him out of baseball for the rest of the season.
The 34-year-old slugger flew with the team to Toronto Sunday night but was scheduled to return to New York to see Dr. Scott Hammer.
Giambi has played in 70 games this season, batting just .221 with 11 home runs and 36 RBI. He has missed for of the Yankees' last five games.
"He told me, 'I don't care about even hitting .220. I just want to feel better,'" his personal trainer, Bob Alejo told the Newark (N.J.) Star-Ledger. "He's exhausted, and it's not getting any better."
"We'll wait and see what the rest of the tests say," Manager Joe Torre said. "He's able to keep food down now, but he's listless. He can pinch-hit for us, but he's limited in what he can do."