Stewart lambasted Christie for his celebration with Jones in the owner's box after the Cowboys 24-20 win over the Lions.
"You lead a state Christie that's half Giants fans, half Eagles fans and you're groping the owner of the Dallas f***ing Cowboys?" said Stewart. "Why don't you just break a copy of Born to Run over the head of a hurricane Sandy victim you backstabbing piece of s***?"
Stewart's commentary was part of a segment looking at potential candidates for the 2016 U.S. presidential election. You can watch the segment in it's entirety or fast-forward to 4:16 to see the section on Christie.
Since Stewart's segment, a report from the Wall Street Journal has suggested that Christie's attendance at the game may represent a breach of his ethics as the state governor.
Christie went to the game in Dallas on the dime of Jones who has a business relationship with the Port Authority of New York and New Jersey. The Port Authority is jointly controlled by Christie and New York state governor Andrew Cuomo.
This presents a potential legal problem for Christie as officials accepting gifts from people who do business with the state is barred by New Jersey law.
A representative for Christie said going to the game was acceptable because the law allows officials to accept gifts from relatives or friends who pay for the gift with their own money.
Jones is a co-owner of Legends Hospitality, a company that will operate an observation deck on the 104th floor of One World Trade Centre which is operated by the Port Authority. The project is expected to generate $875 million in revenue over the next 15 years according to Port Authority officials speaking with the Wall Street Journal. Legends won the rights to the project after a competitive bidding process in 2013.