New signing Nicklas Helenius broke the deadlock at the Ruhrstadion in the second half but Yusuke Tasaka's late intervention levelled the game.
The away side made 11 changes at the break, as manager Paul Lambert continued to run the rule over his charges ahead of the new Premier League season.
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Villa began to open up more after the break and were rewarded almost immediately when Helenius glanced home a header from Leandro Bacuna's cross in the 47th minute, netting his second goal in three pre-season games.
Buoyed by their openeer, Lambert's side twice almost doubled their advantage as first Bacuna went close before Marc Albrighton curled just wide of the post.
As the match headed into the final 15 minutes, Helenius had another effort that flew wide, before Bacuna saw a header cleared off the line.
However, just as it looked like the visitors had the game sewn up, Tasaka curled an effort from the left-hand side into the far post with virtually the last touch of the game.
Villa's pre-season preparations continue with a trip to Lambert's former club, Wycombe Wanderers, on July 20.