Machida has turned down the opportunity to fight on the Toronto card next month so Jones will instead face Brazilian Vitor Belfort.
Jones was initially supposed to fight Dan Henderson on Sept. 1 in UFC 151 in Las Vegas. But Henderson injured his knee and Jones declined a replacement fight with Chael Sonnen, forcing the UFC to cancel the Vegas card.
UFC president Dana White was furious with Jones and his trainer, Greg Jackson, after the UFC was forced to scrap a major card for the first time in his 11 years in charge of mixed martial arts' dominant promotion.
"This is probably one of my all-time lows," White said after announcing the cancellation Thursday. "The one thing that I never thought in a million years would ever happen — it happened."
White said Jones is the first UFC champion ever to turn down a match even on such short notice, calling the decision "selfish" and "disgusting."
Jones (16-1) is among the sport's top handful of pound-for-pound fighters after his meteoric rise to the title in March 2011 in just his eighth UFC fight.
Belfort (21-9) will give up his bout against Alan Belcher at UFC 153 to take on Jones. He hasn't fought at light heavyweight since 2007.
Meanwhile, Dan Miller has been forced out of his UFC 152 fight with Toronto’s Sean Pierson due to a medical issue with his son. The UFC will look for a replacement for Miller. A welterweight bout between Charlie Brenneman and Kyle Noke, which was originally scheduled for UFC 151, has also been added to the Sept. 22 Toronto card.