The Croatian -- who had already been booked earlier in the game -- wasn't shown a second yellow card by referee Michael Oliver for his tackle on Declan Rice in the first half.
"Obviously the VAR can't get involved, second yellows are something that the VAR is not able to get involved in," Webb said on the The Professional Game Match Officials Limited's (PGMOL) Match Officials Mic'd Up programme
"The referee -- one of our best referees, one of the best referees in the world -- Michael Oliver, will no doubt review that."
"I think he was an extremely fortunate player to stay on the field of play."
Webb also said that if Kovacic had been shown a red card for his earlier offence, VAR wouldn't have overturned the decision.
Following on from the VAR error that saw a legitimate Liverpool goal against Tottenham Hotspur disallowed, this is the second successive week in which the refereeing body has found itself under scrutiny.
PGMOL admitted that VAR got the offside decision wrong when Luis Díaz scored what should have been the opening goal in a 2-1 loss for the Anfield side.
Diaz was onside but PGMOL said the goal was chalked off as VAR had "lost sight of the on-field decision" and incorrectly communicated "check complete."
"Having seen what happened in Spurs vs Liverpool we analysed the situation, we had a look at what we can do better to put some safeguards in place," Webb added.
"We worked hard over the subsequent days to look at what we needed to do to put in those safeguards around the communication to avoid that sort of thing happening."
When asked why the referee could not stop the game after play had restarted, Webb said that by the time the VAR and his assistant had realised the mistake it was too late to intervene.
"They recognised that the laws of the game, set by FIFA and the IFAB, doesn't allow that," Webb added.
"There's obviously a process in place that sits in the laws of the game... And it doesn't allow you to go back in those circumstances."
Information from Reuters was included in this report.