The 29-year-old missed City's last three games and both of Argentina's World Cup qualifiers earlier this month after breaking a rib in a his road traffic accident in the Netherlands.
But Guardiola confirmed the Argentine is fully fit for Saturday's (Sunday AEDT) clash against Burnley (LIVE and FREE on SBS at 12:30am AEDT)
"For the game against Stoke he (Aguero) had just one training session. He was fit before Napoli and is ready for tomorrow," Guardiola told a news conference on Friday.
"Normally when we play international games, I make decisions the night before or the same day to see how the players feel."
Aguero has scored six goals in six league appearances this season but there was no indication from Guardiola on whether the Argentine will start ahead of Gabriel Jesus, who has also found the net six times.
The manager added that club captain Vincent Kompany has not recovered from a calf injury he suffered on national duty with Belgium against Gibraltar in August.
League leaders City have netted 17 goals in their last three home matches, including one of the most ruthless attacking displays of the season when they thrashed Stoke City 7-2 last weekend.
Guardiola, however, remains wary of seventh-placed Burnley, who are unbeaten on the road and have collected eight points from a possible 12 at Everton, Liverpool and Tottenham Hotspur and Chelsea.
"We have a lot of respect for what they have done. With the same people and same manager they had problems winning away last season," he said.
"But they've taken points at Anfield, Tottenham and Everton. We have to try and be dynamic and quick."
Sean Dyche's Burnley have returned with a point from two of their last three trips to the Etihad Stadium.