Raheem Sterling's quickfire hat-trick early in the second half set the defending champion en route to a victory that moved the side four points clear of Liverpool at the summit.
But the England winger's opener was initially flagged offside, only for the officials to conclude after a lengthy discussion that the goal should be awarded.
Sterling was in an offside position when Sergio Aguero touched the ball in his direction, but Watford goalkeeper Ben Foster was beaten because defender Daryl Janmaat's challenge ricocheted off the attacker's shin and in.
Even though referee Paul Tierney and his assistant took time to arrive at their decision, Guardiola believes taking that element out of the hands of on-field officials will help when VAR is rolled out in the Premier League next season.
"My first comment is we won because we deserved to win by far. We were the better team on the pitch," he said when asked about the game's pivotal moment.
"It is always so difficult to attack when [Andre] Gray, the striker, is playing the position of the holding midfielder.
"It is so complicated, there are no spaces – just the talent of the players that we have.
"I am so sorry to Javi and Watford if the first goal is offside. But we played an incredible game.
"It's a pity to come here and the first questions are about the referees.
"I don't like it. If he is offside, I prefer he is [given] offside. Like you said, some people say it is offside and some people not. If he is offside, I am sorry."
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Guardiola is a strong advocate of VAR and defended the use of technology even when it resulted in Schalke being awarded two penalties against his team in the Champions League last month.
He explained City was keen for it to be introduced in England's top flight this season, only for consensus with other clubs to prove elusive.
"There is a simple solution. It should be here this season but next season, VAR, and it will be more fair," he said.
" Manchester City voted to install the VAR from the beginning of this season and some other clubs didn't accept that."
Guardiola added: "Next season, maybe VAR is going to solve this situation. We will spend less time than today [discussing decisions] and it will be fair.
"I don't like to lose games for a bad or a wrong decision. The referees want to do a good decision but the game is so quick, so fast.
"If you have doubts sitting here, imagine the doubts for the referee who has one second."
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