Both strikers have been in fine form so far this season, each netting 10 goals across all competitions for the Premier League leaders, yet Guardiola has regularly rotated the pair during an ongoing 16-match winning streak.
The Spaniard revealed that an injury to Benjamin Mendy - from which he may not recover until April - has forced him to pick just one of Jesus or Aguero up front rather than unleashing them both from the start.
"Both have different qualities - they deserve to play. They have a lot of games and they have to be ready. It is the toughest decision," he told reporters.
"Yeah [they could play together] in the moment we had Mendy. When you have Mendy, he can play wide and the winger can go inside.
Aguero has the better strike rate of the two having scored his 10 goals in just 11 appearances, whereas Jesus has 10 in 17.