With Gianluigi Buffon holding the Oranje at bay single-handedly having let Jeremain Lens beat him in the 33rd minute, Prandelli realised his starting strike partnership of Mario Balotelli and Stephan El Shaarawy was just not working.
He promptly introduced veteran Bologna striker Alberto Gilardino and Paris Saint-Germain playmaker Marco Verratti and the two combined to produce a last-gasp equaliser at the Amsterdam ArenA, Verratti scoring his first senior international goal in the process.
Prandelli told FIGC.com: "We played our best stuff when we changed the system.
"Verratti has a big personality and great technique, even if he does like to rush around sometimes. However, he scored a fantastic goal.
"El Shaarawy and Balotelli have to keep working hard together but they have an interesting future ahead of them."
Verratti, 20, pegged the Dutch back and saved Italy from a sixth consecutive friendly defeat when he registered his side's second shot on target deep into stoppage time.
"We managed to get back into the game and I scored my first goal in Azzurro," he said.
"I'm not thinking about earning a starting place, all I want is to do my best and form part of this group.
"I thank my team-mates who've welcomed me into the team. Obviously playing alongside (Andrea) Pirlo is a dream, even if it will be difficult."
Holland might have been out of sight before the break had Buffon not pulled off a string of fine saves, but the Juventus keeper deflected generous tributes on his 124th appearance for Italy.
"It depends on your opponent," he said. "You can have matches where you're a bystander and it looks like you're not giving your all, but it's not the case. We always try to do our best.
"I think the 4-3-3 could still work as we only worked on it for a day and a half, so you can't really make a fair judgement on it."
Holland coach Louis Van Gaal was disappointed with the result but took the time to praise goalscorer Lens, a natural winger, who made the most of a rare chance to start in a centre-forward's role with Klaas-Jan Huntelaar missing through injury.
He told De Telegraaf: "Lens is an option as a striker, of course. We could see that. He held the ball up well.
"Huntelaar's injury gave him the opportunity and he rushed to take it.
"I saw (Dirk) Kuyt at his peak against Germany and now I have seen what Lens can do. That is the purpose of these friendly games."
Oranje veteran Arjen Robben enjoyed his night despite failing to find a way past the impressive Buffon.
The Bayern Munich man was a late addition in the squad when Huntelaar was forced to withdraw and he played 45 minutes on Wednesday night.
He said of Van Gaal: "I am grateful that he always supports me and has confidence in me. It was a wonderful evening."