The 35-year-old went off midway through the second half and could now miss the midweek Champions League game at Valencia.
"It looks like Michael may have broken his nose," Leverkusen coach Robin Dutt told reporters after making a triumphant return to Freiburg where he worked for four years before leaving in the close season.
"This win was a bit lucky. Freiburg played really well after falling behind," he added after the visitors climbed to eighth in the table with 17 points from 11 games.
Germany coach Joachim Low, who brought an end to the midfielder's international career in June, was watching in the stands as the former Chelsea player notched his first Bundesliga goal since scoring for Bayern Munich in May 2006.
Freiburg hit the woodwork through Papiss Demba Cisse in the 38th minute before Jan Rosenthal's glancing header flew narrowly wide.
