The scores were locked at 1-1 after Carlos Tevez had cancelled out Robbie Keane's opener but the tie took a dramatic turn in the 68th minute when Michael Dawson was sent off for a handball in the area under pressure from Wayne Rooney.
Ronaldo stepped and slotted the spotkick into the corner to put United 2-1 ahead and then added his second in the 88th minute when he got away from substitute Chris Gunter and his shot squirmed under goalkeeper Radek Cerny.
"Ronaldo was fantastic again. He took the penalty well and was able to cash in on a mistake late on for the second goal," Ferguson told MUTV.
"His performances have been fantastic and his goals return is amazing.
"But overall perhaps we weren't at the top of our game all over the pitch and some players were a little quiet. But I thought that Ryan (Giggs), who always seems to do well against Spurs, and Tevez played very well.
"It was a very open match and I think it was a fantastic cup tie where both teams contributed to a what was a great game.
"We dominated the possession and we created a number of opportunities but maybe our final ball wasn't as good as it can be which let us down a bit.
"But the most important thing is that we're in the next round.
"Yes, it can be a bit scrappy and you don't play as well as you can, but being in the hat for the draw is the main thing and we've done that."