Giuseppe Rossi gave Italy the lead at Craven Cottage before Nigeria hit back through Bright Dike and Shola Ameobi.
Emanuele Giaccherini struck an equaliser early in the second half as Italy drew for the fourth straight game, extending their unbeaten run to six matches.
Despite failing to claim victory, Prandelli was impressed by his side and said he wanted to see more of the same in future.
"We had a great game, we played football and though the result is penalising, I'd love to see performances like this all the time," Prandelli told Rai Sport.
Prandelli was pleased with the combination of Mario Balotelli and Rossi up front.
The Fiorentina striker scored his first international goal since June 2011 after being played in by Balotelli.
Prandelli said his side needed to look for a second goal after going ahead and lamented what he believed was a push by Dike on Manuel Pasqual in the lead up to Nigeria's equaliser.
"Rossi and Balotelli combined many times," Prandelli said.
"The absolutely terrible mistake we made was that when 1-0 up we tried to hold possession in sterile fashion and we should've looked for the second goal.
"We found more width, found Alessandro Diamanti between the lines. We also did well at the start with four or five passes in a row to get towards the goal.
"The first Nigerian goal was absolutely a foul, but we take home this good performance."
After his team's last game of the year, Prandelli said there were still questions surrounding parts of his squad for the 2014 FIFA World Cup.
"We have many certainties, a few things to consider, which we'll do in time. (Year) 2013 was very positive, as we had a good Confederations Cup and qualified for the World Cup with two games to spare," he said.
"Of course with some results you wanted more, but these lads have done well."
