England's all-time top scorer Rooney came on as a 58th-minute substitute, to roars from the crowd, with the team 2-0 up thanks to excellent first-half strikes from Jesse Lingard and Trent Alexander-Arnold with his first goal for his country.
The game, played in front of a well-below capacity crowd of 68,155, had been billed as a tribute match to Rooney and he was given a guard of honour by both sets of players and received a presentation from the Football Association before kick-off.
Rooney retired from England duty in August, 2017 but the FA decided to turn the friendly into a tribute game for the Liverpool-born player.
The 33-year-old former Manchester United and Everton forward, who now plays in the U.S. for Major League Soccer team D.C. United, did not have a major impact on the game but forced goalkeeper Brad Guzan into a save in stoppage time.
A 54th goal for England would have been the perfect way to bow out but it was typical of Rooney's modest approach to the match that he never tried to create chances for himself, instead showcasing, for a final time at Wembley, his passing ability.
"Tonight was great, a great way to finish my international career, I thought the lads played great. Unfortunately I couldn't get a goal but I'll remember it for a long time," Rooney said.
Callum Wilson, the Bournemouth striker making his England debut, made it 3-0 in the 77th minute to complete a fine night for the debut starters.
Jadon Sancho, the 18-year-old Borussia Dortmund winger, was impressive in his first start, setting up Alexander-Arnold with a well-timed weighted pass for the Liverpool full-back, who drilled home with a fine low shot.
Lingard, one of the few England regulars to start, put in a good performance and his 25th minute goal, a perfect curling shot into the top corner, was a carbon copy of his strike against Panama at this year's World Cup.
England, who face Croatia in a winner-takes-all shootout in the Nations League at Wembley on Sunday, rested a number of regular starters such as striker Harry Kane.
England can top Group 1 in League A with a victory over the Croatians that would take them above Spain into top spot and secure a place in the four-team final tournament next June.
In other international friendly matches on the same day, Germany easily beat Russia 3-0, while Republic of Ireland were held to a bruising 0-0 draw by Northern Ireland; Belgium trounced Iceland 2-0.
