Nemanja Matic's close-range strike salvaged a draw for Chelsea after Agim Ibraimi's goal for Maribor, who were beaten 6-0 at Stamford Bridge two weeks ago.
Eden Hazard had a late penalty saved - but Mourinho felt Chelsea should already have been in front by then, only for substitute Diego Costa to have a strike ruled out for offside.
"Many times surprises happen when people are not fully focused, when they believe the game can't be a difficult one," Mourinho said.
"Only when Maribor scored did the players realise the game was in danger
After that, a fantastic reaction
We deserved to win, clearly.
"We scored two goals, two very good goals
The second goal, the referee (Italian Daniele Orsato) decided to disallow but it's a clear goal.
"Normally we should win because we scored two goals
But we have to accept it.
"We didn't reach the number of goals that we should have in the second half, but the team played well
And we scored a great second goal.
"And the referee's team did not have a good night."
Mourinho admitted he was culpable for not ensuring his players were fully focused at the Stadion Ljudski vrt.
He added: "I was conscious of it, but I was not successful in passing over that message.
"If I cannot convince the players that the game is difficult and you have to play from minute one, obviously it's my responsibility."
The Blues remained unbeaten this season, but could have increased their advantage at the top of Group G to five points with two games to play had they won.
The Slovenians were unrecognisable from the side beaten at Stamford Bridge, but also indebted to goalkeeper Jasmin Handanovic for a couple of outstanding saves.
And Mourinho's men must win in Gelsenkirchen against a Schalke side managed by Roberto di Matteo - the man who led Chelsea to the 2012 European Cup - to ensure progress to the last 16 with a game to spare.
The Portuguese, twice a Champions League winner with Porto in 2004 and Inter Milan in 2012, was happy with an improved second-half showing after a poor opening 45 minutes.
He said: "The first half we were not good
Very slow, no intensity, no creativity.
"In the second half we played very well, but they scored
When they scored the situation was a bit more difficult for us.
"After that I thought we played magnificently: creative, fast, good dynamic, lots of chances to score
By that, we deserved to win.
"But I think it's fair to praise Maribor's efforts because they gave everything
They fought with everything to try to get the point."
Mourinho had introduced striker Costa and Oscar at half-time, hauling off Willian and Andre Schurrle.
The Blues boss was critical of his players after the Capital One Cup win at Shrewsbury and the Premier League defeat of QPR, but he held his counsel after the latest insipid display.
"I tried to improve my team," he said.
"When you try to improve your team, sometimes it's for tactical reasons
Other times it's for individual performances.
"I think I was successful with the changes I did
In the second half the team were much better than in the first half."
Maribor had already drawn with Sporting Lisbon and Schalke; now they have three points after holding last season's semi-finalists.
Maribor boss Ante Simundza said: "We had an exceptional game, a fantastic spectacle here in Maribor.
"We played a fantastic match and we proved that we deserve to be in the group stage of the Champions League.
"It could've turned out differently for us
We could've lost this point as well, but we are satisfied."
Source : PA