Gundogan headed in from Kevin de Bruyne's corner after fourteen minutes and completed the scoring after half-time with the pick of the goals - a curling effort into the far corner of Tomas Vaclik's net.
The German spent most of last season on the sidelines with a cruciate ligament injury and has struggled to recapture his pre-injury form this season, scoring just two goals prior to Tuesday's brace.
“Gundo is an extraordinary player," Guardiola told the club's official website. "Last season we missed him a lot when he was injured. Not just his goals, his personality to play, he was fantastic. I am so happy for him.”
Bernardo Silva and Sergio Aguero scored City's other goals as they cruised to a victory which effectively renders the second leg at the Etihad Stadium a dead rubber. Guardiola urged caution, but also admitted that his side were on the verge of the quarter-finals.
“Four-zero away - it’s amazing result, but the Champions League is 180 minutes in total,” said the Spaniard.
“We are almost there in the quarter-finals. I’m not saying it’s done but we’ve had an amazing result. We defended the long balls quite well, but we were clinical today. It’s not easy to keep the level we have been playing at, but we did it. Overall, I’m delighted."
Guardiola has been insistent that Manchester City will not win the quadruple, but they are still in all four competitions and are favourites to win at least three of them. They lead the Premier League by sixteen points, face Arsenal in the League Cup final, and travel to Wigan in the fifth round of the FA Cup this weekend.