Foden has been limited to just one start, in the League Cup against Preston, so far this season as the return of Kevin De Bruyne and signing of Rodrigo has seen the England under-21 international fall further down the pecking order.
But he made the most of barely a few minutes on the field against the Croatian champions after being introduced as a substitute in stoppage time to fire home after fellow sub Raheem Sterling had opened the scoring.
"I know he deserves to play. I want to give him minutes, every time he doesn't play I am completely unfair to him, I'm sorry," said Guardiola.
"But Kevin De Bruyne is there, David Silva, Bernardo Silva, Rodri, (Ilkay) Gundogan. It's what it is.
"I know the best way to grow up is play minutes and minutes, but he is so young.
"I don't know how many players of that age played as many minutes in the recent past he played in these last seasons with us.
"He is going to be an incredible future player for us because we count on him and we trust a lot in him."
Guardiola keeps cool after Jesus complaint
Sterling even hopes Foden will get enough chances to shine to make a late run to be included in the England squad for next year's European Championship.
"I am buzzing for Phil and I want him in the national team," said Sterling. "If he keeps going he will be there."
However, City' local hero Foden is happy to play a patient game with such an array of midfield talent to compete with.
"You have to show the manager what you can do each day in training," said Foden. "Every young kid wants to play but you have to keep patient."
City enjoyed 71 percent possession and had 19 attempts on goal, but had to wait until 24 minutes from time to make the breakthrough when Sterling rounded off an excellent team move.
The English champions have maximum points from their opening two games with back-to-back matches against bottom-of-the-group Atalanta to come.
"It was good. We didn't concede one shot on target, with our huge possession we created enough chances to score earlier, but we were patient," added Guardiola.
"We need two more victories to qualify for the last 16 and hopefully we can make against Atalanta almost the definitive step to be there."
Despite missing the injured De Bruyne, Sergio Aguero, Bernardo Silva and David Silva were all guilty of missing guilt-edged chances before half-time, while Gundogan hit the bar.
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Dinamo had romped to a 4-0 victory over Atalanta on matchday one, but barely ventured over the halfway line and their brave resistence was finally ended with a wonderfully worked team goal.
Rodrigo's pass opened up the Zagreb defence and Riyad Mahrez's low cross left Sterling with the simple task of forcing the ball over the line from point-blank range.
That should have alleviated City's frustrations for the night, but Guardiola was shown a yellow card by Dutch referee Serdar Gozubuyuk and cut an increasingly annoyed figure on the touchline as the hosts saw a number of penalty claims turned away.
"Nobody is going to give us anything," said Guardiola. "We did it ourselves and that's top. That's why I love this team."
There was little for the Catalan coach to be concerned about, though, as City were never in danger of conceding and finally made the game safe deep into stoppage time when Sterling led a counter-attack and teed up Foden to blast into the far corner.
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