Yorke pounced for his 18th goal of the season just when Alan Curbishley's struggling Addicks looked to have hung on for a crucial point towards their relegation dogfight.
Charlton battled every step of the way in search of their first win in 12 Premiership games. But there was no way back once substitute Paul Scholes crossed for Yorke on the back post to nod the ball past the despairing dive of Simon Royce.
In their last game, Charlton enjoyed a last-minute equaliser to earn a point against Newcastle to end a run of eight straight defeats. This time, though, the last-gasp goal at the Valley was not so welcome as the Reds flexed their Premiership muscles.
Charlton had started confidently in a game which took time to wake from its Sunday slumbers. Both teams enjoyed spells of possession in midfield, but the goalkeepers did not have to earn their corn until the last 10 minutes of the first half. First Charlton's Royce saved well from Ryan Giggs and then reacted well to turn a Denis Irwin cross behind after more good play on the left by Giggs.
Nicky Butt whistled a long-range drive a foot wide of the post, and Royce leapt to his left to tip a vicious Giggs volley round the post.
The Addicks produced some neat pockets of football, but goal attempts were limited. Mark Kinsella dragged a 25-yard effort wide, and referee Gary Willard turned down two penalty appeals in first-half stoppage time. The first came when Martin Pringle collapsed under a Henning Berg challenge as the pair battled for a John Robinson cross.
Then moments later Willard was alert to spot Peter Schmeichel had got a hand to the ball as he raced from his line to beat Kinsella to a long pass.
The big Dane was less convincing when he made a hash of the resultant corner. He flapped at Kinsella's kick and watched thankfully as Neil Redfearn smashed the loose ball over the bar from 12 yards. Andy Hunt chose to go it alone after the break when he had team-mates well placed in front of goal. He had been found by a clever Redfearn pass and made a yard for a shot that lacked power, and Schmeichel saved.
The experienced United goalkeeper plucked a good chance from Hunt's head moments later as the Addicks striker shaped to finish a sweeping move.
Redfearn found Robinson, whose deep cross was headed back into the danger zone by Pringle, but Schmeichel read the situation and dispelled any threat. Curbishley's men had to soak up a lot of second-half pressure as United turned up the heat in search of a winner. Nicky Butt, Gary Neville and Giggs all crashed shots over, and Royce survived under a barrage of corners and crosses. Then Butt poked a shot horribly wide after linking up sweetly with Andy Cole inside the area.
The pressure built up, and finally the Addicks defence snapped. Scholes collected a ball on the right and turned his cross to Yorke who leapt high to head home off the foot of the post.
Charlton Athletic: Royce, Powell, Redfearn, Rufus, Kinsella, Hunt, Robinson, Brown, Jones, Tiler, Pringle. Subs: Bright for Hunt, Parker for Pringle
Manchester United: Schmeichel, G Neville, Irwin, Stam, Berg, Beckham, Butt, Giggs, Keane, Yorke, Cole. Subs: Solskjaer for Beckham, Scholes for Butt Scorers: Yorke (89)
Referee: G Willard
Attendance: 20,043