Rooney made his first public appearance of pre-season - featuring for the first time other than in a behind-closed-doors game with Real Betis - following hamstring and knee injuries for 67 minutes at Wembley.
The 27-year-old's future has been the subject of much conjecture with Chelsea having had two bids rejected.
Welbeck would not be drawn on Rooney's future, but was pleased to see his club-mate back in action.
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."
Welbeck scored England's second equaliser, from a Steven Gerrard cross, before Rickie Lambert, Rooney's replacement, netted the winner in the first England-Scotland fixture in 14 years.
Welbeck added: "With Stevie putting balls in you've just got to try to get into dangerous positions. I did that today, thankfully.
"It was an occasion you won't forget any time soon. The atmosphere was brilliant.
"You could feel the passion from the stands - it really drove the lads on."