Stones and Silva are leaving Man City once their contracts expire after a combined two decades of service to the club.
The pair have been instrumental during Pep Guardiola's era of dominance at the Etihad Stadium, with the Spaniard also calling time on his 10 years in Manchester.
To thank Silva for his unforgettable nine years at City, the club decided to hold a guard of honour on the hour mark, which both sets of players took part in as he exited the pitch.
But Rooney disagreed with it taking place during the game, and said he would have been "fuming" if he was Aston Villa.
"It’s incredible, I’ve seen a few things this season, and it just makes me sad that some of these things are happening in football," Rooney said on BBC Sport's Match of the Day.
"Bernardo Silva, John Stones have been incredible for Manchester City and they deserve it, but do it after the game. If I was in that Aston Villa team, I’d be fuming.”
The duo didn't get the ending they wanted at the Etihad as City lost 2-1 against Aston Villa thanks to an Ollie Watkins brace.