Liverpool and Chelsea currently occupy the remaining Champions League spots, but only six points separate second from fourth.
During his stint on Sky Sports' Monday Night Football, the ex-United captain claimed that North London rivals Tottenham and Arsenal are likely to miss out.
"I think Chelsea are a great team. I think they will make the top four definitely," said Rooney. "I think obviously there seems to be a few issues with Conte but I'm sure they'll get sorted out and they've got enough quality there to finish in the top four.
"You'd think [United will make it]. It's tight, Tottenham have come into it, Liverpool. So it is going to be tight, two of those big six teams are going to miss out. I just think Chelsea, Man City, I fancy Liverpool and Man United."
Rooney's Everton currently sit 10th in the standings.