The Dutchman was booked late in last Sunday's 1-1 draw against Hamburg for time-wasting which earned him a yellow card, but he was shown a second yellow - and the compulsorily red - when he made an obscene gesture to the referee.
The German Football Association (DFB) gave him a three-match ban for his action, but the 30-year-old insists he was responding to Hamburg fans in the Allianz Arena crowd.
He will now appear in front of a DFB disciplinary committee in Frankfurt to explain his side of the story. The committee's chairman will then make a final ruling on the matter. But the evidence against van Bommel is concrete - television cameras clearly showed him making the gesture while staring at the referee Lutz Wagner who saw what was happening as he turned round.
Van Bommel, known for his fiery temperament on the pitch, will definitely miss Saturday's clash with Schalke 04 in Gelsenkirchen as a red card automatically carries a minimum one-match ban.