Stephan Andersen spilled a slightly deflected shot by Wayne Rooney shortly after the half-hour, Scholes tucking in the rebound.
A goal was inevitable, United dominating the first half so comprehensively it seemed Charlton thought they were holding out for a point at Old Trafford.
The second goal began with Charlton losing possession cheaply. Rooney skipped down the left and pulled the ball back for Scholes, who teed up Darren Fletcher to sidefoot in from 20 yards.
Charlton briefly ventured out of their half in the second period but were sliced up on the counter-attack. Rooney hit the post after being set up by Smith, then Smith charged down Talal El Karkouri's clearance to score his first goal of 2005. Finally Rooney claimed the goal he deserved after a slick interchange of passes concluding with Kleberson's through ball.
This could have been a wonderful day to be a Charlton fan. The Valley wallowed in nostalgia as awards marking the club's centenary were made to former players such as Sam Bartram and Derek Hales. Perhaps they should have brought their boots. Charlton have been "on the beach" since January, winning just one of a dozen matches since then.
This defeat effectively ended any hopes of a first appearance in Europe. There is the faint prospect of a place through the Fair Play League but even this modest aim was jeopardised with five minutes left when Chris Perry was dismissed for clumsily hauling down Wes Brown.