Courtois has been the regular number one for the Premier League leaders this season, but was left on the bench for the meeting at Stamford Bridge.
Cech was in impressive form, producing two key saves from former Chelsea man Romelu Lukaku, and Mourinho explained his decision to rotate his goalkeepers for the game.
"Courtois played consecutive matches, against Liverpool, Manchester City and Aston Villa, games where he needed to be very focused," he told Chelsea's official website.
"Every detail is so important, even when he doesn't touch the ball, the focus must be permanent and I think a goalkeeper can also be tired. The tiredness isn't just physical, it's also from your nervous system.
"Petr has been working really well and hard. In every training session I was getting the feeling his condition was magnificent. Tonight he was the best option for the team, also in terms of leadership.
"John Terry was ill this morning and he was probably out of the game until the last minute, so I thought I needed Petr's personality and capacity to communicate at the back. The decision was good."
