Ferran Torres and Alvaro Morata lined up up front for Spain, while Cristiano Ronaldo led the Portuguese with Diogo Jota and Joao Felix among their attacking options.
Jose Fonte had a first-half goal disallowed for a push while Torres nodded wide at the far post from Morata’s cross.
Morata had two good second-half opportunities before Ronaldo headed wide on the 70-minute mark from Bruno Fernandes’ delivery.
Spain boss Luis Enrique hailed his new defensive partnership of Aymeric Laporte and Pau Torres after the clean sheet.
“I have seen the two starting centre-backs as sensational, they were superb,” he told a post match interview with Marca.
“They both played a game bordering on the outstanding.”
He added: “It was a very good test for us and I think we will all be ready for the European Championship.
“In the first 60 minutes we managed to almost completely cancel out the reigning European champions, they almost didn’t make three passes in a row.”
Spain are in Group E alongside Sweden, Poland and Slovakia, while Portugal have a tough group with Germany, France and Hungary.
Elsewhere, Italy won 4-0 over Czech Republic, while Hungary edged Cyprus.