Farrell was taken to the hospital on Thursday night after experiencing discomfort in the left side of his chest. He was diagnosed with pneumonia and has been away from the team since.
"Still feeling a little shaky, so we made the decision that he will not be with us in the Baltimore series," Blue Jays acting manager Don Wakamatsu said. "We'll evaluate him and see when he'll be able to return at that point once we're on the road."
Farrell arrived at Rogers Centre on Monday afternoon to be examined by the club's medical staff. He is improving, but hasn't reached the point where he has been cleared to make a return.
General manager Alex Anthopoulos met with the first-year manager after he was examined and the decision was made for Farrell not to make the trip on Monday night to prepare for a three-game series in Baltimore.
The club remains optimistic that Farrell will join the team in New York on Friday, but it's still too early to know for sure.
"I think he came in today thinking he was going to try to manage but he's still a little weak," Wakamatsu said. "Just to be safe, this is not something you want to play around with obviously and just make sure [we] get him back on his feet."
It was initially believed that Farrell would be out of action for only a couple of games. Despite the recovery not progressing as quickly as Farrell initially hoped, the Blue Jays said there isn't anything severe taking place.
"I think it's one of those things where you just don't know," Wakamatsu said. "Obviously with pneumonia you got to be awfully careful, but he felt good enough to come in today to make sure he gets checked out and we just want to be safe with it."