Ivan Perisic and Pepe struck for their sides as Croatia’s first match since their World Cup final defeat by France ended in a draw.
Perisic had volleyed in from close range in the 18th minute to put the visitors in front, before Pepe, who scored in his country’s last-16 loss to Uruguay in Russia this summer, headed in Pizzi’s cross on 32 minutes
Portugal’s Cristiano Ronaldo missed the game after declaring himself unfit.
Sergio Oliveira and Gedson Fernandes won their first caps after coming on as second-half substitutes for the visitors.
Croatia are now without retired goalkeeper Danijel Subasic and striker Mario Mandzukic, while influential midfielder Ivan Rakitic was rested for the game.
Both countries begin their Nations League campaigns next week.