Germany international Goetze has fully recovered from the ankle injury he picked up three weeks ago and trained on Tuesday with the team in the final session before Wednesday's game.
"He needs time because he was out injured for a long time and then got injured again," Guardiola told reporters. "We will decide tomorrow if he will be included in the squad."
The midfielder, brought in from Borussia Dortmund for 37 million euros (£31.2 million) in a surprise transfer coup, has yet to put in a run at Bayern following a muscle injury in Dortmund's Champions League semi-final against Real Madrid.
After recovering in August, he sustained an ankle injury in Bayern's Super Cup win over Chelsea last month.
Guardiola, who also has midfielders Thiago Alcantara and Javi Martinez still out injured, said he was running low on options.
"I cannot really rotate in midfield. We have problems there with the many injuries."
Bayern last season became the first German team to win the treble, after clinching the domestic league and Cup double and adding the Champions League title as well.