Both players have been key signings for the Gunners so far this season, with Mikel Arteta's side sitting top of the table.
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Reigning champions City are five points below them in second spot, and closing the gap has proven to be more difficult than expected.
Despite potentially aiding Arsenal's title chances, Guardiola has no regrets over the departures of Zinchenko and Jesus.
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Speaking ahead of the two sides' FA Cup clash on Friday, he said: "Why? Because they are winning.
"They have been amazing for us, we have incredible respect for them as people first and as footballers.
"Of course we want to beat them, but all the success they've had, I'm more than delighted. Both clubs agreed and that's all."
Zinchenko may have been affected by injury this season, but he has still made a solid impact in the 15 matches he has featured in so far.
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Jesus has five goals and seven assists to his name in 20 appearances, but hasn't played for Arsenal since November due to his recovery from a knee injury he sustained at the World Cup with Brazil.
City haven't necessarily struggled without them, but it's clear that Arsenal have improved with the duo.
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They will compete for a spot in the last-16 of the FA Cup, with both sides being two of the strongest teams left in the competition.
In February, they will compete in their first hotly anticipated Premier League clash.
A win for either club would have a huge effect on this season's title race, with Arsenal and City set to remain as the two favourites to go for glory.
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