Dortmund said that Hummels, 25, suffered a mid-foot sprain in Tuesday's match and that he would be out of action for about two weeks.
The Germany international had been out since November due to an ankle injury suffered in Germany's 1-0 friendly win over England at Wembley and only returned to Dortmund's lineup for a 2-1 Bundesliga win over Braunschweig on Friday. His ankle injury has healed completely, Dortmund said.
Hummels will miss Saturday's match at Werder Bremen, the German Cup quarter-final at Frankfurt next week and a Bundesliga game against Frankfurt. He could be back for Dortmund's Champions League quarter-final trip to Zenit St Petersburg.