A bizarre Graeme Shinnie own goal killed off 10-man Aberdeen's hopes as they suffered a 2-1 aggregate defeat in Slovenia.
After a 1-1 draw at Pittodrie, McInnes' team knew they had to score against the Slovenians if they had any hopes of making the play-off round.
But Adam Rooney missed a penalty midway through the first half and substitute Jayden Stockley was sent off for two bookings before Shinnie's attempted back pass bounced over the foot of goalkeeper Joe Lewis and into his own net.
After the game, McInnes criticised Bulgarian referee Nikola Popov's display.
He said: "The referee was really poor tonight. Football is a contact sport.
"Right from the outset he blew his whistle at the slightest moment of contact. It never allowed any flow to the game.
"I thought the sending off was ridiculous. I don't think you see that decision in any other country.
"Stockley is just trying to use his arms for leverage at the second booking. There is no movement with the elbow.
"We were frustrated at the penalty award.
I think the referee should have allowed (Niall) McGinn to carry on and put the ball in the net. He was very quick to blow.
"You could say the Rooney penalty miss is defining but we still had to overcome the officials.
"I think the officials played the biggest part in all the defining moments tonight.
"I thought the result was very harsh on my team. I thought we had a lot of good play.
"I can't remember Adam Rooney missing a penalty before. He is so dependable from 12 yards out. We don't apportion any blame to him.
"He has made the difference for us and won us games before and will do so again.
"It was a horrendous bobble for the own goal too. It has come up six inches off the ground. I don't apportion any blame to Joe Lewis. It was the pitch."
Source: PA
Source: PA