Mourinho believes a third goal would have killed the tie ahead of their next week’s second leg at the Stadion Maksimir in Zagreb.
The Portuguese coach fielded a strong team in an attempt to blow the visitors away in the first leg and rightly started on the front foot but could not get an early goal.
Harry Kane put the hosts ahead on 25 minutes before he got the second goal on the 70th minute mark when he pounced on Kevin Theophile-Catherine’s failure to clear the ball properly.
Speaking to BT Sport after the game Mourinho said: "I believe one more goal would be a good reflection of the game and would put us in a much better position.
“But before the game if you asked if 2-0 was a good result I would say. It is only a good result if we do the job there. It will be a difficult match. At home they will feel more comfortable to have a go with nothing to lose.
Kane was replaced by Carlos Vinicius on 84 minutes due to injury but Mourinho has revealed the England superstar’s injury is nothing serious and will be ready for the North London Derby against Arsenal on Sunday.
"Harry I don't believe is anything big. Sunday is a match everyone wants to play and little things will not stop him. I don't have the feeling it is anything serious,” the former Chelsea and Manchester United coach added.
"He is doing everything. He is doing the striker job of scoring goals. the team work of creating space and linking play and the extra work not many strikers do in defence.
“He helps us a lot. He has an incredible number of clearances from crosses and corners. We couldn't be happier.
“I gave a rest to many of the players and am so happy with what Vinicius is giving us. But with Harry on the pitch it is a different story for us."
