"He is going to try to do the best job, like we try as managers and football players", said Guardiola when asked about the referee at his pre-match press conference.
But while he stopped short of criticising Mourinho, the 37-year-old said the style of football employed - Anthony Martial's penalty was United's only shot on target - would not go down well with fans if the results were not good.
Benjamin Mendy revealed Manchester City's players issued themselves with a half-time warning to prevent a repeat of last season's derby collapse.
"We deserved the win because the guys up-front made an wonderful job, created chances, got into the box and scored goals".
"We nearly didn't give United any chances bar the penalty", the Portuguese said.
"Pep's in his third season here, it's my second and I can see the team has a deeper understanding of his ideas".
"Every player was saying the same thing: 'OK, guys, don't do the same as a year ago, be careful, pay attention.' So when we came back on the pitch, we played better than the first half, so won the derby". I don't think too much.
"One thing is a bad performance another thing is a performance with mistakes".
The United manager made the comments after he saw his side lose 3-1 away at Man City.
'Now I feel much better and to be able to score my first goal was really incredible'. There's a number of performers in that City team he has worked really hard on.
"The bottom line is, United's recruitment hasn't been as good as City's".
"You can go for stats, that's the way people who don't understand football analyse football", said Jose Mourinho after Sunday's 3-1 defeat by Manchester City.