The Manchester United striker was handed the boot by 77-year-old Bobby Charlton, star of England's 1966 World Cup-winning team, whose record of 49 goals Rooney surpassed with a penalty in last month's 2-0 win over Switzerland.
The boot, mounted on a plinth, was carried to the side of the pitch by a British serviceman before Charlton presented it to a smiling Rooney as chants of "Rooney!" echoed around the stadium.
Rooney, 29, was present at Wembley despite an ankle injury having ruled him out of the game, as well as England's final qualifier away to Lithuania on Monday. England have already qualified for the tournament.