Guardiola saw his side go in 2-1 down at the break against Schalke thanks to two Nabil Bentaleb penalties, the first of which was awarded after a three-minute delay to check a handball by Nicolas Otamendi - who was booked and later sent off.
Referee Carlos del Cerro Grande, who was unable to re-check the incident due to faulty pitch-side screens, was at the centre of the uncertainty.
Technology had earlier helped City take the lead through Sergio Aguero after Schalke appealed for a foul in the build-up to the goal.
But after Leroy Sane's stunning free-kick and Raheem Sterling's 90th minute winner, Guardiola was keen to praise the VAR.
"I am a big fan of VAR," the Spaniard told the media after the 3-2 success. "It's a penalty. The second one is a penalty too. Offside too. And the red card can be a red card.
"The result is good, but it’s not over. Hopefully, our fans can help us in the second leg and hopefully, we can improve."
VAR also overshadowed Atletico Madrid's win over Juventus, after Alvaro Morata's header was chalked off for an apparent foul on Giorgio Chiellini.
City rode their luck on the way to take a significant advantage into the second leg.
After Bentaleb had cancelled out Aguero's opener, the ex-Tottenham playmaker doubled his tally again from the spot after Fernandinho had felled by Salif Sane.
Otamendi was dismissed on 68 minutes but Sane's brilliance drew the Premier League champions level before Sterling' late intervention.
Guardiola added: "I am delighted with the performance. We came here to sit back and defend? No way!
"The opponents didn't do too much. The opponents are good my friends.
"They have the quality to create problems. And they didn't do too much. We played 20 mins 10 v 11."