"Ells didn't play a lot the last couple of weeks of Spring Training," Girardi said. "I'm going to guard against overplaying him early."
Brett Gardner moved to center field, with Alfonso Soriano taking over duties in left field and Ichiro Suzuki playing his first game of the season in right field.
"Joe just let me know last night, but I'll be available, ready to go," Ellsbury said. "He let me know it was going to be either tomorrow or today, so after [Wednesday's] game, I let him know I was good to go. I'll be ready if I need to come into the game at some point today."
Girardi said that the travel schedule factored into the decision; the Yankees expect to get settled in Toronto after 5 a.m. ET on Friday, so Girardi had planned to sit Ellsbury for either the third or fourth game.
Brian McCann was also out of the lineup on Thursday against Astros left-hander Brett Oberholtzer, but he is slated to catch Masahiro Tanaka on Friday in Toronto.
Girardi also elected to play switch-hitting rookie Yangervis Solarte at third base over left-handed-hitting Kelly Johnson, saying that Johnson is scheduled to play all three days against right-handed starters at Rogers Centre.
"We're just kind of mixing up," Girardi said. "We've got a tough schedule these first couple of weeks; 13 days out of the get-go."
Girardi hinted that Derek Jeter would get a day off during the Toronto series, possibly on Friday. Mark Teixeira will also rest a day in Toronto, and the plan is to have McCann be the designated hitter on Saturday.
"We're two games in and we're not where we want to be, but you can't say, 'We've got to keep running them out there,'" Girardi said. "If you end up getting them hurt and you end up missing them [for] three weeks, that's really not good for us. With the schedule that we've got, I have to be a little bit proactive with these guys until we get through these 13 days."
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.