The Red Devils came out on top 2-1 at Old Trafford but Cisse impressed after coming on as a second-half substitute, scoring one and then hitting the crossbar with an overhead kick late on.
Speaking afterwards, Ferguson said: "I'm very pleased, first to win the tie in an all-Premier League clash but Newcastle had a stronger team than us physically. We played fantastic football and I think we deserved it.
"Cisse is a terrific player. Our defence handled it well. We want to progress as far as we can. Winning is always important to this club."
The draw for the fourth round of the competition took place soon after the full-time whistle at Old Trafford and United next face a trip to Chelsea.