United conceded after just three minutes when Martin Petrov put the Premier League visitors ahead.
Paul Hayes levelled, and the Iron battled right until the final moments when Robinho - for whom the Brazilian side Santos have made an enquiry, which City will address at a board meeting this week - scored to make the score 4-2.
"I'm pleased for the players who have worked hard and made it an entertaining cup tie against the might of Manchester City and the players they have brought here," he said.
"We all had a belief that there was a giant-killing in the offing but it just wasn't to be. We got off to a bad start but credit to the players they didn't buckle. They regrouped and kept going and conceded a goal on the stroke of half-time that can deflate anybody. But they came out in the second half and gave it a right good go.
"You've seen the way they break - they're like the Red Arrows at times - and that's the difference between the very top and where we are."
Roberto Mancinin, the CIty manager, was relieved to have avoided an upset in his first taste of the competition.
"The FA Cup is very difficult, we saw that today [Sunday] with Arsenal and Stoke. Every game will be hard and the next game against Stoke will be a difficult game," he said.