The 31-year-old - recalled to the starting XI after missing three games with a thigh injury - scored in the seventh minute of his 543rd United appearance to move alongside Charlton, having played 215 fewer games than the England great.
Rooney, who joined United from Everton in 2004 and scored a Champions League hat-trick on his debut against Fenerbahce, turned home Juan Mata's cross, before celebrating the landmark strike with a fist-pump in front of watching Charlton and former boss Sir Alex Ferguson. United went on to win the match 4-0.
Meanwhile, Arsenal fresh from grabbing a memorable 3-3 draw at Bournemouth after going behind 3-0 in their last league match, came from behind again this time to snatch a 1-2 away win at Preston North End in their Saturday third round Emirates FA Cup tie.
Giroud who scored a late equalizer was at it again this time scoring his fourth goal in four games since returning to the starting line-up, sinking the impressive Sky Bet Championship side with a deflected 89th-minute effort in the third-round tie at Deepdale.