Rooney has not featured for United in any of their pre-season matches and also missed the weekend victory over Wigan in the Community Shield, as rumours of his Old Trafford exit persist.
But the 27-year-old featured for 67 minutes of England's 3-2 victory over Scotland at Wembley, and Welbeck praised Rooney's contribution.
Welbeck, who was named man of the match, said: "It's really good to link up with him. I've been playing with him for a very long time now.
"Once we're on the pitch we know each others' games. I'm just really happy for him to get out on the pitch and get his first game of the season.
"We all know the quality Wayne Rooney possesses. To have him on the pitch for Manchester United is a bonus."