Former Blues and Wimbledon midfielder Jones suggested Villas-Boas would not be in complete control of matters at Stamford Bridge with Terry around.
England captain Terry has failed to get to grips with his new manager's tactics this season, while the 30-year-old is also the subject of a police investigation into claims he racially abused QPR defender Anton Ferdinand, something he denies.
Terry is arguably the most influential figure in the Chelsea dressing room and Jones said that may not be a good thing as Villas-Boas attempts to completely revamp the club's style of play.
"Honestly, I wouldn't be surprised if JT moves on," he told BBC Radio Five Live.
"Sometimes, you've got to clear the decks.
"You think, 'How can you leave someone like JT out?'
"But sometimes your big, high-profile players go and other players come in and, all of a sudden, the coach is in charge again."
Jones, who compared the situation at Chelsea to that Sir Alex Ferguson encountered when he took charge of Manchester United 25 years ago, also believes the Terry racism inquiry is unsettling the club.
"That's all got to be sorted out," he said.
Chelsea have lost three of their last four Barclays Premier League games to lie 12 points adrift of Manchester City and pile the pressure on Villas-Boas.
Jones urged notoriously trigger-happy Blues owner Roman Abramovich to stand by his manager but admitted the club's own fans could turn on the Portuguese if his revolution continues to falter.
"They made a bold statement putting such a young fellow in charge of such a high-profile club and I think that Abramovich has got to stick with it, especially until next season," he said.
"He has to to show face.
"I think he's definitely going to give him some time, I really do.
"If you look at the guy's record, he's going to make decisions that the fans are not going to be happy with.
"If a coach comes into a new club and makes decisions that fans are not happy with, but gets the results, they go with the coach.
"It's as simple as that.
"If results don't go the right way then they start shouting for his blood."