The championship bout, which was scheduled to headline a UFC event in Sacramento, Calif., is expected to take place at a future date.
Fox Sports reported the injury earlier Monday.
A flyweight title fight between Demetrious Johnson and Joseph Benavidez, originally scheduled to headline The Ultimate Fighter 18 Finale on Nov. 30 in Las Vegas, has been moved to the Dec. 14 event at Sleep Train Arena.
It's the second time this year that Pettis, 26, has been forced to postpone a fight due to a knee injury. He was scheduled to fight UFC featherweight champion Jose Aldo in early August but withdrew after hurting his knee during a training session in Brazil.
Pettis (17-2) was then booked to a lightweight title fight against Ben Henderson at UFC 164 on Aug. 31. He claimed the belt via submission in the first round.
Thomson (20-5) earned the title shot with a second-round TKO over Nate Diaz in April, his only appearance of 2013. Thomson leap-frogged the injured TJ Grant, who has been out with injury since August after suffering a concussion in training.
A lightweight fight between former No. 1 contenders Diaz and Gray Maynard will headline the TUF 18 Finale. The bout was originally slated as the co-main event.