Balotelli incensed Ferdinand and his United team-mates after the final whistle by thrusting the badge on his shirt in the direction of opposition supporters.
Ferdinand, writing on his Twitter account the morning after the game, said: 'If you score a goal and give a bit to opposing fans I kind of accept that but at the final whistle (you should) go to your own fans and enjoy it, not opposing fans.'
Up for the cup: Balotelli celebrates after City's victory over United
Balotelli also winked sarcastically at Ferdinand as the players left the field and the pair had to be separated by their team-mates.
Ferdinand added: 'If I offended anyone, I apologise, emotions obviously running high.'
The defeat ended United's bid for the treble and Ferdinand urged his team-mates to bounce back by winning the Barclays Premier League and Champions League.
'Disappointed we didn't get the win we were looking for,' he said. 'Now let's go and win some silverware.'
Flashpoint: Ferdinand tries to get to City striker Balotelli at the end of the game
Ferdinand did have something to celebrate after his wife gave birth to his first daughter.
The defender dashed 200 miles to Cheshire at 2am and was just in time to be at wife Rebecca's side for the birth before racing back to London for the match.
He said: 'We had a baby girl named Tia Ferdinand! Want to thank the ambulance service and all the Wythenshawe Hospital staff for helping my baby arrive safely.'
Making his point: An angry Ferdinand (left) with Patrice Evra and Anderson (right)
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Explore more:People: Rio Ferdinand, Mario Balotelli Places: Manchester, London