Sterling swept home from a Riyad Mahrez cross midway through the second half, then set up 19-year-old Foden in stoppage time as City’s second successive win took them top of Group C.
Guardiola said: “He (Foden) has incredible finishing and made an incredible step forward tonight.
“I am so sorry for him – he deserves to play more minutes. I am sure he will contribute and help us more.”
The England squad for the next round of internationals is named on Thursday.
“I am buzzing for Phil Foden,” Sterling told BT Sport. “I want him in the national team. If he keeps going he will be there.”
Foden said: “You have to show the manager what you can do each day in training. Every young kid wants to play but you have to keep patient.”
In truth, this should have been a much bigger victory, with City wasting a host of first-half chances, but in the end they were grateful to Sterling for making the difference.
Until he broke the deadlock from close range with his ninth goal of the season, it had been an unexpectedly frustrating night for Guardiola’s side, despite enjoying more than 80% of possession.
It was not the case that City struggled to create chances in the absence of the injured Kevin de Bruyne, but they were unable to take them until the second half.
Sergio Aguero was the first to waste an opportunity, with the Argentine rounding Zagreb keeper Dominik Livakovic from a poor backpass but seeing him recover with a diving save.
Bernardo Silva was also off target from two good openings and Aguero skied another effort before Ilkay Gundogan blasted a shot against the bar and David Silva fired wide from close range.
When Aguero did finally get the ball in the net, Dutch referee Serdar Gozubuyuk had already blown his whistle for a handball by Bernardo Silva.
The second half saw Croatian champions Dinamo, who were roared on by their fans throughout, put up more resistance before Sterling replaced Bernardo Silva, and quickly gave City their breakthrough.
More chances followed but it fell to Foden to finish off Zagreb with a fine first-time strike from a swift counter-attack.
It gives City their second successive Group C win and leaves them well placed to make the last 16 for a seventh successive season, while Zagreb have now suffered 13 away group game defeats in a row – a Champions League record.
