Jota fired home the only goal just before the hour mark at Anfield as Liverpool opened up a 12-point lead at the top of the Premier League.
Luis Diaz had been in an offside position when James Tarkowski cut out a pass towards the Colombian.
But Diaz then pounced on the loose ball to tee up Jota to drill in his first goal since January.
Everton boss David Moyes said he was disappointed to lose a derby to a “clearly offside goal”.
However, Slot said the officials did get the decision right as the rules stand given Tarkowski deliberately played the ball.
“It was not offside, according to the rules,” said Slot.
“Do I like the rule? No, I don’t like the rule. I hate that rule but the execution of the rule was fortunately for us today well done in that situation.”
The goal was the second highly controversial call of the game after Tarkowski avoided a red card just 11 minutes in for a wild lunge on Alexis Mac Allister.
The Everton captain was given a yellow card by referee Samuel Barrott, who was not instructed by VAR to review his original decision.
Slot said he did not need to comment on the decision as so many others had spoken out on the challenge.
Former Manchester United captain Gary Neville described it as a “leg breaker” in his role as a pundit commentating on the match.
Even Moyes accepted that Tarkowski was lucky to stay on the field.
“Since I have seen it, we could have been lucky we didn’t get a red,” said Moyes.
“It looked a high one. I think it was the follow through that looked worse.“
