It came three minutes from time from Demba Ba, who became an unlikely hero in a season where he has found match action limited.
Mourinho revelled in the success - a 2-0 win on the night earned a 3-3 aggregate draw, with Chelsea progressing on away goals - and lauded all aspects of his side's performance.
"The players were open to the risk, they were open to the sacrifice," Mourinho told Chelsea TV.
"People in midfield they had to run miles
People in the defensive line, they had to cope with these big players with lots of space, which is always more difficult.
"People who create were always trying to create
The strikers went to the box well.
"Fantastic mentality by the boys and so, so happy for them."
Mourinho, twice a Champions League winner, had questioned his players' attitude following the loss at Crystal Palace and was again critical after the Parc des Princes defeat.
But they appeared to be a different proposition at Stamford Bridge, where they have now claimed nine consecutive clean sheets.
Whoever Chelsea draw on Friday, Andre Schurrle believes the Blues have a chance of emulating their 2012 European Cup triumph.
Schurrle, who scored the opening goal after replacing Eden Hazard after 18 minutes, said: "Every team in the semi-finals can win this.
"It's one step to go to the final
We'll see who we get and we'll see if we can go through.
"We're looking forward to the draw and then to the matches."
When Hazard, Chelsea's most potent attacker this season, departed with a calf problem which is likely to rule him out of Sunday's match at Swansea - and possibly for longer - the hosts' chances looked bleak.
But Schurrle scored within 14 minutes of his introduction and produced a man-of-the-match display.
"We put everything we had into this match," the Germany forward added.
"To win in the end is an unbelievable feeling."
Mourinho feared the winning strike would not come after Schurrle and Oscar hit the crossbar in quick succession in the second half.
The Chelsea boss said: "Against good teams we don't create so many chances and when you hit the bar twice it comes into your brain that maybe you cannot do it.
"One minute later you believe again that you are going to do it."
There was collateral damage from the win, with Branislav Ivanovic picking up a yellow card which means the Serbia right-back is suspended for the semi-final first leg.
Cesar Azpilicueta will likely be switched to right-back and Ashley Cole will come in at left-back, while midfielder Ramires will be available again after a one-match ban.
Domestic competition is the immediate priority, however.
Following the defeat at Palace, Mourinho conceded defeat in the Premier League title race as Manchester City have games in-hand and Liverpool are two points ahead.
But there could be twists and turns aplenty with five games to go.
The Champions League semi-final matches take place either side of Chelsea's trip to Anfield, which is scheduled for April 27.
First Chelsea go to the Liberty Stadium looking for a first Premier League away win since the defeat of Fulham after successive losses at Aston Villa and Selhurst Park.
"Now we have (a place in the Champions League semi-finals) we can enjoy and at the weekend show that we can win away in the Premier League," Schurrle added.
Source : PA
Source: PA