In one final heartstopping twist deep into five minutes of stoppage time, City's packed stadium celebrated what they thought was a last-gasp tie-clinching hat-trick goal by Sterling.
Spurs manager Mauricio Pochettino has been one of the few bosses to question whether the technology is a risk to the spirit of the game and to his credit, he still maintained a degree of skepticism even after his team benefited so much from VAR.
This followed a 10-minute passage without a goal - nearly like an eternity in comparison, before Raheem Sterling scored again and put the host side in the lead.
But the drama was far from over and from a corner, Spurs regained an aggregate lead when Fernando Llorente bundled home from close range and despite a lengthy VAR check, the referee gave the goal.
"I watched the action and the people from above decided it was offside", Guardiola added.
The home side were later struck again by VAR, although the decision appeared incontrovertible.
However, a VAR review showed Aguero had been fractionally offside in the build-up when the ball fell to him after Silva blocked Christian Eriksen's pass, taking City from ecstasy to agony and leaving their quadruple dreams in tatters. Sterling thought he had won it in injury time - sparking wild scenes of celebration - only for VAR to rule his strike out for offside. "Those are the rules and we have to respect them", Mendy told City's website.
Moussa Sissoko says he did not realize Tottenham had qualified for the Champions League semi-finals at Manchester City's expense.
"It was unbelievable the way the game finished".
"He [McNeil] has been here long enough to see that happen to other players, hopefully he'll take it as one of those things", said Dyche.
The South Korea forward, who now has 11 goals in 11 games with England striker Harry Kane absent, said: "I have never seen something like this, it was a very tough game, a very insane game".
City didn't deserve to lose this game, but somehow, over two legs, we have.