The Swede avoided a second bookable offence for a late challenge on Liverpool full-back Kostas Tsimikas before going on to score the only goal of the tie's first leg just moments later - much to the annoyance of Slot and his players.
The Reds boss said: "When he didn’t give the second yellow, I didn’t think anyone would think it would have such a big impact 30 seconds later.
"I think the referee was probably also like, is this happening? For him, it was also far from ideal. I am 99.9 per cent sure that’s what he thinks because I can’t look in his head and he didn’t say how he felt.
"It was a good goal. Let that be clear, ball in behind, cut back cross and Bergvall stayed calm to score and finished it off. I don’t think you are interested in that but the moment before."
Liverpool defender Virgil van Dijk also bemoaned the "mistake" by the referee.
He said: "It was quite obvious there was gonna be a second yellow.
"It was pretty clear, and then a minute later he scores the winner. Listen, it is what it is. [The referee] made a mistake in my opinion and I told him that. He thinks he didn't. It was quite obvious and everyone on the sideline knew it."
The loss was only Slot's second defeat since taking charge of Liverpool but he admits that the 1-0 deficit is "far from ideal" for his team heading into next month's second leg.
The coach said: "The good thing is there is a second leg but it’s a far from an ideal position for us. They are a good team and will probably have some players back for the second leg."