Substitute Antonio Di Natale put the Azzurri ahead on the hour mark moments after coming on but Cesc Fabregas soon hit back for Spain, who introduced Fernando Torres late on and could have snatched the win if the striker had been sharper.
"The draw was fair. We need to improve," Prandelli told a news conference.
"We really tried to press the Spaniards from the start of their attacks. We tried to avoid one on ones and for 60-70 minutes I think we played very well at the back.
"What disappoints me was that we allowed them to equalise very quickly. We should have made them work harder to get back into the game. The problem we had with Torres is that we gave him the ball twice. We caused problems for ourselves."
Prandelli, who raised eyebrows himself by handing a debut to Emanuele Giaccherini at left wing-back in a new 3-5-2 formation, had expected Torres to start.
"We were a little surprised that there was no stirker but we decided to play as we had planned," added the coach, whose side had lost their last three friendlies.
Mario Balotelli had a fitful game and was replaced by Di Natale soon after running clear on goal but failing to shoot or pass before being tackled.
"When he missed that chance I already had decided to bring on Di Natale. We needed to be a bit better going forward, it was not a punishment at all," Prandelli said.
"I just wanted one of the strikers to go deeper. Mario just has to remember how he created that chance, he pressed, won the ball back and created it."
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