Stanton, who also missed Game 2, strained his right quadriceps while running to first base in Game 1.
Yankees manager Aaron Boone stated that Stanton is available off the bench, according to MLB.com's Bryan Hoch.
"He wants to play," Boone said. "But we've also had some real conversations about, 'You've got to be honest with where you're at.' I mean, there is an injury in there."
Boone added that Stanton would be put on the injured list if this was the regular season.
After appearing in just 18 season games for the Yankees this year due to myriad injuries, Stanton recorded six at-bats against the Minnesota Twins during the division series. He then homered against Houston in Game 1.
If the Yankees remove Stanton from their ALCS roster, he'd become ineligible for the World Series.