Giuseppe Rossi put Italy ahead but goals from Bright Dike and Shola Ameobi saw African Nations Cup champions Nigeria leading at the interval.
However, Sunderland forward Emanuele Giaccherini made it 2-2 soon after the re-start to ensure the Azzurri avoided defeat in their last game of 2013.
Prandelli felt they should have signed off the year with a win though, saying: "We have played a great game. We created so many goalscoring chances.
"We made the mistake not to double our lead after going ahead having had several chances to do so.
"I think the result penalises us as I would always want to see my players produce these type of displays."
Prandelli, who celebrated his 50th game in charge of Italy against Nigeria, was pleased with the performance of strikers Rossi and Mario Balotelli.
Balotelli provided the assist for Rossi to put the Azzurri in front but wasted a hatful of chances to get on the scoresheet.
"I liked how Rossi and Balotelli played in attack," Prandelli said. "They immediately found each other."
The game at Craven Cottage offered Prandelli a chance to evaluate certain candidates to complete his World Cup squad.
Prandelli fielded an experimental defence against Nigeria and was pleased with what he saw.
"We have several months to go before the World Cup and I have a lot of certainties," Prandelli said. "I still have a few thoughts to consider and I will do that.
"In any case, 2013 has been very positive."
Italy came third in this summer's Confederations Cup after edging Uruguay in a penalty shoot-out while the Azzurri finished their World Cup qualifying campaign unbeaten.