St Pat's went out fighting but failure to take chances put an end to their European run.
Tempers boiled over on the final whistle in Tallaght after CSKA overturned a 1-0 aggregate deficit to progress 2-0 on the night and 2-1 overall.
Saints midfielder Jamie Lennon and CSKA’s Bradley De Nooijer squared up to each other after the final whistle and it sparked a melee involving most players.
READ MORE: St Patrick's Athletic pay the penalty for wasteful finishing as CSKA Sofia get to gloat at full-time
De Nooijer was sent off after the final whistle and so too was St Pat’s midfielder Adam O’Reilly who passed up two great scoring chances earlier in the game.
Lennon, so impressive in the engine room, said: “It was just frustration from the players. Their man was celebrating in front of our fans and I don’t really like that.
“Looking back it’s probably a compliment to us.
“They were probably rubbing their hands after the Mura game, the fact that it was us, they were probably thinking it would be easy to get through play-offs.”
CSKA progress to play Swiss giants Basel in next week’s playoff round with St Pat’s - who are still €750k the richer for the experience - left to refocus on the league.
Saints boss Tim Clancy said: “We wouldn’t have been favourites in Mura but the players were outstanding for the four games we’ve had in Europe this year.
“It’s with pride that we go out. It’s not the case that we’re going out with a performance that we’re not happy with or frustrated with how we played.
“It’s just unfortunate that we’re sitting here at the end of the fourth game in Europe and we’re frustrated more than anything else.
“We’ve spoken about it in there but it starts against Sligo Rovers on Sunday - trying to get back into Europe next year.
“That was our priority at the start of the year and hasn’t changed.”
Clancy slammed his team’s defending for the opening goal from a 12th minute corner, but cried foul when CSKA won a late penalty after Harry Brockbank handballed.
“The officials won't have to come out and explain why a free kick is given in front of the dugout. I have no idea why it was,” said a bemused Clancy.
“We have seen it on the video and it looks like it hits their player’s hand first before it comes back onto Harry’s.
“Again, the referee is really quick to put the whistle in his mouth and give the bigger club a decision.”
Asked if he spoke to the officials, Clancy said: “No it’s not worth your while. It was chaos after the game. A load of stuff going on. I don’t know what happened.
“I went in to speak to them afterwards, but I wasn’t allowed.”
Clancy added: “It was a huge effort to try and go through against a hugely established team in European football but it’s a sore one as I think we had the best chances.
“But at this level of European competition these are the chances that you have to take.”
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