Mourinho admitted that his team's display was below par, but the Portuguese believes that his charges were worthy of the three points at Stamford Bridge.
"It was a completely deserved victory, but not a good performance," he told Sky Sports News. "We had good periods, and some moments of good reaction to negative periods, but I didn't think we played a complete game like normal.
"So why do we deserve [to win]? We deserve it because we had lots of chances and Eden was a player who gave a fantastic performance, but in reality they were a team who had great defensive organisation.
"They put in a very difficult situation to face but we have to play better. They changed their system and defended well. We couldn't score the third goal to win the game and kept them in it too long."
The Premier League leaders travel to Liverpool next week.