Reds team-mate Wayne Rooney also started the friendly match at Wembley, clocking up 67 minutes, before Wilfried Zaha and Phil Jones added to their international cap collections as late second-half substitutes.
United boss David Moyes attended the match as a pundit for live broadcaster ITV. Afterwards he commented: "I thought Danny and Tom did very well. Danny got his goal tonight and showed what he's capable of.
"Wayne grew into the game as it went on. I think the important thing was he got some playing minutes. That bodes well for us and it will hopefully start to get him ready for when he's available and fit to play."
Rooney was replaced on the field by the scorer of England's winning goal, Rickie Lambert. The Southampton striker notched decisively with his first touch, powering in a header from Leighton Baines' left-wing corner to put the hosts in front for the first time.
Welbeck also scored with his head in the second half, converting a free-kick from Steven Gerrard, as England came from behind for the second time in the match following a fine effort by Scotland's Kenny Miller. In the first period, Arsenal's Theo Walcott answered James Morrison's opener when he raced onto Cleverley's superb first-time pass into the right-hand channel.
Welbeck almost claimed a dream Wembley double just past the hour mark when his acrobatic volley flew fractionally wide. Shortly afterwards, Cleverley joined Rooney in departing the fray, but the game