In 2006 Bonderman finished with a 14–8 record, his career best and posted a 4.08 ERA. He started game four of the 2006 American League Division Series against the Yankees. He pitched five perfect innings before giving up a hit. He then pitched 3 more innings, surrendering only one run. Bonderman was the winning pitcher in the game that gave the Tigers the series. He pitched again in game four of the 2006 American League Championship Series, pitching six innings and giving up three runs. The Tigers would go on to win the game and series for the American League Pennant. In the World Series, he pitched six innings giving up two runs. He left the game with the Tigers in the lead. However, the Tigers would ultimately lose the game, as well as the series the following day.