The midfielder is battling to overcome a chronic bowel complaint and was back in action along with Wayne Rooney, who returned after a thigh gash sustained last month
He said after his side set up a fourth round tie at Chelsea: "It's great to be back, it's been a long time so it's just good to be back, especially at Old Trafford and back in a winning team as well."
Portuguese star Anderson lashed home a superb 44th-minute opener and when Tom Cleverley added the home side's second in the 58th minute, Sir Alex Ferguson's side seemed to be home and dry.
But Magpies substitute Papiss Cisse came off the bench to reduce the deficit in the 62nd minute and almost grabbed a stunning equaliser when his overhead kick struck the bar.
On the performances of Fletcher and Rooney, manager Ferguson said: "Excellent, both of them. Wayne obviously tired towards the end, but that was to be expected.
"I'm very very pleased, they've done very well. They've all done very well."
Capital One Cup fourth round draw: Sunderland v Middlesbrough, Swindon v Aston Villa, Wigan v Bradford, Leeds v Southampton, Norwich v Tottenham, Liverpool v Swansea, Chelsea v Man Utd, Reading v Arsenal. Ties week commencing October 29.