Van Bommel only joined Milan in January from Bayern Munich and despite being sent off in his first game, his combative presence became a major asset for the Rossoneri.
The 34-year-old had been linked in the media with a move to England with his short-term deal at Milan running out but he has opted to give Serie A one more year.
Milan are still mulling whether to offer veteran midfield trio Clarence Seedorf, Andrea Pirlo and Massimo Ambrosini new deals.
Reserve goalkeeper Flavio Roma has also signed for another year.
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