The England international has heaped praise on the 36-year-old, who announced his retirement on Tuesday, and aired his opinion that Lionel Messi might struggle to shine in England
Scholes, who made his last appearance for the club in Saturday's Champions League final defeat to Barcelona, announced his retirement on Tuesday after making 676 appearances for the Red Devils.
"He'll be missed greatly. I just heard the news this morning," Rooney told talkSPORT.
"We knew he'd make a decision but didn't think it would be this quick. We're all sad to see him stop playing.
"He's been great for United and England and he'll be missed by all of us.
"He hasn't started that many games of late and I'm sure that's come into his head and he's made his decision."
The former England international will join United’s coaching staff next season and Rooney admits his old team-mate's absence will be felt by players and fans alike.
He added: "But he'll be a big miss for us. He's the best I've played with and against.
"He's only small but it's so difficult to get the ball off him. Every United fan will miss him."
Rooney also reflected on his side's 3-1 defeat at the hands of Barcelona at the weekend and admitted that United were outplayed.
"It hurt," he said. "I watched the game again because you can always learn by watching football.
"It was very disappointing but you have to put your hands up and say they were the better team.
"They are the best team I’ve seen and Lionel Messi the best player.
"I think he got three nutmegs in the first-half. On my Playstation I can make him do what I want but he’s even better in real life.
"The speed he moves his legs, in fact his whole body, is amazing. Messi wins them games but Xavi and Andres Iniesta destroy you."
The United man also conceded that Barcelona are the team to catch, adding: "They are simply a fantastic team, a very special side.
"That’s the level we want to be at and we have to up our game to achieve this. The manager will be doing what he can to see we do this."
Despite praising Messi, Rooney believes the Argentine might struggle in the Premier League.
"If you bring Xavi and Iniesta with him, yes [he could be a success]. But it would be difficult, almost impossible for him to play as he does in Spain,” he said.
"The game is more physical here, going to the likes of Birmingham and Stoke away is very demanding.
"Cristiano Ronaldo is more suited to the English game than Messi. Cristiano is taller and good in the air."