The 55-year-old started them in last night's 1-1 draw with the Netherlands, but said that the former Manchester City striker needs time to regain fitness.
"They obviously need to work together," Prandelli told RAI Sport. "Mario knows he's not in great shape and needs to recover, but we have an interesting future to work on."
Marco Verratti scored a late equaliser in Amsterdam to save Italy from what would have been a seventh straight friendly defeat.
Prandelli added: "We didn't want to lose and we didn't want to concede.
"Obviously the 4-3-3 system is particular and we need time to work on the details, but I saw interesting things in the first half. We need more character, as we have the players with the right qualities."
Italy's next match is a World Cup qualifier against Malta in March.