Terry was give a four-game ban by the English FA on Thursday after being found guilty of racially abusing Queens Park Rangers defender Anton Ferdinand in a Premier League match last season.
Former England skipper Terry, who retired from international football last Sunday, is yet to decide whether to appeal.
"Chelsea had a squad in which we had 12 African players," Real Madrid manager Mourinho, who led Chelsea to two Premier League titles, said in an interview with CNN shown on Saturday.
"It was a fantastic squad and he had always a great relation with every one of them. Please don't say he is a racist, because I know what I am saying.
"[Former Chelsea players] Didier Drogba will say, Geremi will say, Claude Makelele will say, all of them will say he is not a racist."
Terry was cleared of racism in a court of law in July but the FA's decision to press ahead with their own case against him was followed by his decision to quit playing for his country.
While supporting his former skipper, Portuguese coach Mourinho did not try to deny that Terry had abused Ferdinand.
"It can happen that during a football match - because sometimes it's more than a game - sometimes you have reactions that don't represent what you are really," Mourinho said.
"Probably, he had a racist comment or attitude against an opponent and, sometimes in football, we look to our opponents in the wrong way. But to pay, he has to be punished."
Terry played in league leaders Chelsea's 2-1 victory at Arsenal on Saturday because his ban will not take effect until he has decided whether to appeal.
