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.
The home side dominated for long stretches and missed several good chances.
Ballack was on target after two minutes as he volleyed in from close range after Freiburg failed to clear a corner.
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.
They went close again in the second half with Leverkusen keeper Bernd Leno denying Stefan Reisinger twice from close range and Cisse firing over the bar.
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