The Dutchman, 44, has paid the price for a run of seven games without a win, Saturday's 2-0 reverse at home to Freiburg making it three straight defeats in the Bundesliga - the first time in nine years they have had such a run.
"Ultimately, there were more factors separating us than uniting us," said Wolfsburg's managing director Jörg Schmadtke on the club's website on Sunday.
"There was a lack of conviction in terms of being able to get out of the difficult situation we're in and turning things around as quickly as possible, which led to us making the decision to end our working relationship. We wish Mark all the best in his personal and professional life."
Van Bommel's record with Wolfsburg reads 13 games, four wins, three draws and six defeats, with those wins coming in the first four games of the Bundesliga season.
He leaves with Wolfsburg bottom of UEFA Champions League Group G with two points from three games.
"I'm surprised and disappointed by the decision because I'm certain that we would have managed to get back on track together," Van Bommel said. "I hope the team manage to turn things around quickly."
Wolfsburg are yet to announce who will take the reins for next Saturday's trip to Bayer Leverkusen and a key Champions League tie with Salzburg three days later.