The Bayern Munich boss does not want his star man to rush back from injury after making his comeback in midweek in the 5-0 win over Hamburg
The Germany international made his comeback on Wednesday after recovering from ankle surgery, and completed 25 minutes as the Bavarians beat Hamburg 5-0 in the quarter-final of the DFB-Pokal.
However, the Spaniard does not feel that his star midfielder is yet able to feature from the start.
"It's still a bit too early," he said at a press conference on Friday.
"He's an outstanding player. I hope that he can improve every day and every game so he gets his fitness."
Bayern face a Champions League trip to Arsenal on Wednesday but Guardiola was keen to deflect attention away from their European exertions.
"I don't know where that'll be in our heads. The next game is always the most important."
Guardiola also pointed out the threat posed by Christian Streich's side who recently claimed the surprise scalp of Bayer Leverkusen.
"They're very aggressive. This isn't fun, but work. We have to run, run and run."
Bayern and Freiburg kick off at 15:30CET at the Allianz Arena on Saturday.