The Wolves boss revealed Webb had been in contact with the club this week and admitted they had made the wrong call when not punishing Nick Pope's challenge on Raul Jimenez.
Jimenez was brought down by goalkeeper Pope at 0-0 in the first half, but referee Andrew Madley waved away appeals for a penalty and VAR did not intervene.
National and local media were unified in their condemnation of the decision with Newcastle legend Alan Shearer also admitting his side had been very fortunate.
"They have apologised to us - it's happened and now it's passed," said Lopetegui.
"Howard (Webb) has said sorry and this is done now. I have to trust and I do trust in the referees.
"It's very hard work, it's very difficult work, but we have a limited energy and we have to put this into our daily efforts and nothing else.
"We don't get the points back and now we have to look for more, starting with Leeds."
It's the second time Webb has had to apologise to the club in less than eight weeks.
Ironically, Madley was also the referee when VAR failed and Wolves were denied a memorable winner against Liverpool in the FA Cup in January.
"We have to have trust in the referees and technology, it's not in our hands - we can only affect what we do on the pitch.
"This year we have been very unfortunate with some of the decisions but we have to continue to trust in them."
Lopetegui says all the focus is on the huge 'six-pointer' clash with Leeds.
"Each match is a big challenge and a chance to get three points - that's where our focus needs to be.
"We have to be 100% vs Leeds, it's so important.
"We have to do our best, each match is very different and we have to be at our top level against a very good team."
Meanwhile Lopetegui had mixed news on the injury front ahead of the crucial clash at Molineux.
Hwang Hee-Chan will miss the game after picking up a new unspecified injury following his goalscoring return.
Boubacar Traore is now back in first team training, but will not be available for selection until after the international break.
But there was better news with the Wolves chief confirming Pablo Sarabia is fit after being ruled out with a heel injury last weekend