The result means that Italy can still progress to the knockout stages if they avoid defeat against Uruguay in their final group match.
Prandelli believes that his side gave everything they could, but could not match the aggressive approach of their opponents.
"It was a defeat where Costa Rica were much more aggressive and played with passion," Prandelli told RAI Sport. "We already knew this was a particularly tough group and that we'd have to gamble our qualification in the last game with Uruguay.
"We thought that we'd find a third midfielder, but never did. If we had scored, then perhaps it would've been a different game, but we deserved this defeat.
"I don't know if we were superficial and it would be a huge mistake if we were. The players ran hard and in these conditions gave all they had."
Italy's defeat in Recife means that England have been knocked out of the tournament.