1. Joe Hart
2. Nathaniel Clyne
5. John Stones
6. Phil Jagielka
3. Luke Shaw
7. James Milner 58'
4. Jonjo Shelvey
11. Alex Oxlade-Chamberlain 67'
8. Ross Barkley
9. Jamie Vardy
10. Wayne Rooney 59'
Subs
15. Gary Cahill
17. Fabian Delph 58'
19. Ryan Mason
14. Theo Walcott 67'
16. Michael Carrick
18. Harry Kane 59'
21. Kieran Gibbs
12. Chris Smalling
13. Jack Butland
20. Raheem Sterling
22. Tom Heaton
Rooney looked set to pass Charlton's record when he scored his 49th England goal from the penalty spot in the 12th minute.
But in a bizarre move, Hodgson took Rooney off in the 58th minute, therefore robbing him of a chance to bring up his 50 in the 6-0 win.
Cristian Brolli scored an own goal and Ross Barkley headed in his first England goal before Theo Walcott grabbed a couple off the bench and Harry Kane netted to seal the win.
After an embarrassingly early World Cup exit, Hodgson has done incredibly well to make it to Euro 2016 with three matches to spare.
After seven wins from seven, the Three Lions are the first team to qualify, and have gone 12 matches unbeaten for the first time since 1996.
But the main talking point from the game will be Hodgson's decision to take Rooney off with the record so close.
The 29-year-old will now have to wait until Tuesday's home game against Switzerland to bring up his half-century.
Rooney hardly made the best of starts. The forward dropped deep to pick up a pass off Jamie Vardy, but his attempted backheel did not find the intended recipient.
That all changed for the skipper in the 12th minute, though.
While jostling for position in the box, the referee spotted a push by Marco Berardi on Rooney in the box as James Milner swung over a free-kick.
The Cypriot official pointed to the spot, which caused consternation among the San Marino players. They surrounded the referee, but he stood by his decision and also showed a yellow card to Berardi.
The England captain chuckled to himself and almost apologetically placed the ball on the spot before tucking the ball away.
The England fans chanted Rooney's name as he looked to the sky, with both arms aloft before turning to wave at his wife Coleen and eldest son Kai, who had made the trip to the Stadio Olimpico in Serravalle to watch.
England toiled for a while. The recently relaid pitch had started cutting up after just a few minutes and the ball did not roll smoothly at all.
As expected, the Sammarinese were making England it hard for England to attack. They lined up with five at the back, but whenever England had the ball, their formation turned to 7-2-1.
England found a second goal, but again there was a touch of fortune about it. Luke Shaw drove the ball towards the box after making a run down the left and Brolli turned the ball into his own net.
Aldo Simoncini denied England a third just before the break by tipping over Alex Oxlade-Chamberlain's shot.
But 15 seconds after the restart Barkley nodded in the Arsenal winger's cross to make it 3-0.
Ten minutes later Joe Hart made his first contribution, saving a looping deflected shot.
Boos were heard as Hodgson swapped Rooney for Kane with 32 minutes left.
Walcott added a fourth by converting a cross from fellow substitute Fabian Delph and Kane chipped the goalkeeper to make it 5-0. Walcott then rounded off the route with a calm finish.