The Leicester winger had set his heart on a move to City in January but it failed to come off and the Algerian was left licking his wounds, refusing to return to training with the Foxes.
That led their boss Claude Puel to hit out at City and the way they handled the situation but Guardiola has defended the club's behaviour.
'I think the club made a statement and it was so clear what happened," said Guardiola.
"The club made a statement and always tries to do the best for us and, of course, respecting the opponents.'
Meanwhile, Mahrez returned to action for Leicester in their FA Cup win against Sheffield United on Friday night and received a standing ovation from the club's fans.