The substitute turned in Fabio Cannavaro's header with an outstretched arm eight minutes from time and the referee only gave a free kick after furious Dutch players asked him to consult his assistant.
Chances were limited with John Heitinga heading wide for the visitors midway through the second half just after Fabio Grosso had wasted a good opportunity for world champions Italy.
The two coaches fielded strong lineups but would have learnt little as they plan for June's World Cup in South Africa.
"What I can't explain is the percentage of passes we misplaced in the first half. It was a bit better in the second, 0-0 is not great but we are satisfied," Italy coach Marcello Lippi told Rai television.
Home goalkeeper Gianluigi Buffon picked up his 100th cap while Livorno midfielder Antonio Candreva impressed on his debut and Cagliari's Davide Biondini also made his first appearance.
Injured Dutch striker Robin van Persie was carried off in the 15th minute while Inter Milan playmaker Wesley Sneijder was ruled out before kick-off with a thigh problem.
An Italy fan ran on to the pitch early on with a T-shirt calling for Sampdoria's Antonio Cassano to be brought into the team having been continually overlooked by Lippi.
The game was played in the Abruzzo region as part of a fundraising drive to help victims of the earthquake which killed nearly 300 people there in April.
Italy host Sweden in another friendly in Cesena on Wednesday while the Dutch meet Paraguay.
