Mourinho was seemingly unhappy with referee Paolo Tagliavento, who sent off defense duo Walter Samuel and Ivan Cordoba before half time.
However, the Portuguese coach defended his act by denying he was confronting the referee.
"That handcuff gesture was misinterpreted," Mourinho’s spokesman Eladio Parames told Italian news agency ANSA.
"It had nothing to do with the referee. He meant to say a different thing: ‘You can even take me away and arrest me, but my team is strong and will win regardless, even if we play with nine men."
Inter's nine men helped Mourinho maintain his superb 130 unbeaten home games, dated back from his spell with Porto.
Inter said they will appeal against Mourinho's ban and 40,000 euros fine, as well as suspensions for Sulley Muntari and Esteban Cambiasso.