The promising youngster headed United in front in the remarkable game against Arsenal but had to limp off later in the first half with Javier Hernandez taking his place.
Rooney was sad to see Welbeck also miss out on a likely England squad place with some reports suggesting he could be out for around four weeks.
"It's a shame," Rooney told MUTV. "He's been playing really well and got another goal. I'm sure he would have been in the England squad so it's a big shame.
"Hopefully he gets back soon enough. When he does, he will score goals. He is going to be a very important player for us this season."
Ashley Young added his sympathy for his colleague in a separate interview with MUTV, stating: "Obviously it's sad to see one of your team-mates go off and hopefully he'll have a speedy recovery.
"We don't know how long he's going to be out for now. He was terrific up to that point. But there's competition for places and I'm sure someone will come in and fill his boots."
Rooney, meanwhile, revealed he's been practising his free-kicks in training, along with Young and Nani.
"It's something we've been working on," he added after sending two searing shots past Arsenal goalkeeper Wojciech Szczesny. "Me, Youngy and Nani in training for the last few weeks.
"I was unlucky against Tottenham and got two that went in against Arsenal thankfully. Nani and Youngy are good free-kick takers as well so it's