A struggling Newcastle, who had no shot on target during the match where they led thanks to Palace defender Marc Guehi's own goal, settled for a point after Daniel Munoz equalised in added time.
"It was a contact injury, not a muscle pull, which is good news for us. We hope he will recover quickly but at this moment I don't know," Howe said about Isak.
Injuries to strikers have hindered 10th-placed Newcastle throughout this season, with England international Callum Wilson missing four months with a back injury.
Wilson, who returned to action in Monday's 2-0 loss to West Ham United, was not ready to come on in the first half to replace Isak, Howe told the post-match press conference.
"Obviously, he has minimal training time and I have to be really, really careful I don't push him and lose him," he said. "So I didn't feel bringing him on at that stage with the minutes we had left of the game was something I could do."
Howe rued the continued impact of injuries in the team's performance ahead of a difficult December.
"We look a bit low on confidence and losing Alex was a huge blow to that," the manager said.
Newcastle host leaders Liverpool on Wednesday.