The visitors took the lead, with Ivan Perisic volleying in from close range in the 18th minute.
But Pepe, who scored in his country’s last-16 loss to Uruguay in Russia this summer, headed in Pizzi’s cross on 32 minutes to earn the home side a draw.
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, who also had Wolves midfielder Ruben Neves and Southampton defender Cedric Soares in their starting XI.
Croatia, beaten 4-2 by France in the World Cup final in July, 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, with Portugal hosting Italy in Group A3 on Monday, while Croatia are in Spain on Tuesday in Group A4, which also contains England.