The Italian, who won the Champions League as Blues manager, argues that the Premier League champions are not the types to sanction sales of their best players to rivals
The 43-year-old argues that it would be impossible for the England striker, for whom the Blues have had two bids rejected, to end up at the London club because "United never sell their best players to rivals".
"Rooney is a top-class striker and a fantastic player, who can play for any team in the world, but I don't think Manchester United will allow him to join Chelsea. United are well known for not allowing their top players to join rival teams, especially in England," Di Matteo told Goal.
"He would definitely perform very well at the Bridge if he ends up moving but it would be one of the most shocking transfers should he join Chelsea."
United manager David Moyes has continually stressed that Rooney will stay at Old Trafford but Chelsea boss Jose Mourinho has declared that their pursuit will continue until the end of the transfer window.
Di Matteo, who was in Kenya to launch a new fantasy game dubbed Guinness Football Manager, insists that he does not hold any grudge against Blues owner Roman Abramovich, who sacked him despite winning the Champions League and FA Cup titles in 2012.
"Most successful managers have been sacked, so I have great company there," he joked. "It's part of the experience. I'm now looking forward to winning many more things ahead.
"It was a fantastic experience working under him. Abramovich had his own opinion so sometimes we had to agree and sometimes disagree but, at the end of the day, we had to move on. He gave me the opportunity to serve the club and did my best and I am now looking to the future."
The Italian says that he is not looking to make an immediate comeback to the dugout, despite several clubs making contact with him.
"I'm going to take this year off," Di Matteo confirmed. "I've received many offers but I have to take a rest, regain all my energies before I return to coaching. I want to travel across Central Africa with my new role as the ambassador for Guinness and I will think about coaching after one year."