The visitors outclassed San Marino’s part-timers as they chalked up a seventh successive Group E qualifying win to seal a place in France next year with three matches to spare.
Rooney, who scored his first goal for England 12 years ago this weekend, equalled Charlton’s 45-year-old record when he scored with a 13th-minute penalty, sending goalkeeper Aldo Simoncini the wrong way.
Both players scored their 49 goals in 106 appearances.
The England skipper never had another clear-cut chance to break the record and manager Roy Hodgson replaced Rooney after 57 minutes with Harry Kane who also got among the scorers with a well-taken chip in the 75th.
“It’s a proud moment for me to equal Bobby’s record and my aim is to push on and help the team beat Switzerland on Tuesday,” Rooney told ITV Sport.
“Since I joined Manchester United, Bobby gives me advice after games and I am sure if anyone will be happy for me to break his record it will be him.”
Hodgson said he had always planned to take Rooney off.
“It was in our thoughts to keep Wayne on for 45 to 60 minutes because other players needed to play,” the manager explained.
“We played well today and players like Jonjo Shelvey had a good game on a very difficult pitch.”
San Marino, who have only avoided defeat in a competitive match once in 10 years, played some neat football but there was never any doubt about the outcome even before Cristian Brolli headed a cross into his own net after 30 minutes to double England’s lead.
Ross Barkley made it 3-0 seconds after halftime when he nodded his first goal for his country and the second half turned into little more than a training match as Hodgson’s men retained possession for long periods.
Substitute Theo Walcott, who had just replaced Arsenal team mate Alex Oxlade-Chamberlain, tapped in the fourth goal at the far post in the 68th minute.
Kane, without a goal for Tottenham Hotspur this season, ended his drought with a perfectly-flighted effort over Simoncini before Walcott slid in the sixth goal in the 76th minute.
Switzerland and Slovenia, who are second and fourth in the group, meet later on Saturday.
(Reporting by Mike Collett; Editing by Tony Jimenez)