Ronaldo looked more frustrated than he had in other matches.
His 33 passes were the third fewest of the Portugal starting XI, although he did provide the crucial assist for Quaresma.
Another substitute Renato Sanches drove forward with the ball and found Nani, who in turn laid the ball to Ronaldo at the far post.
Playmakers Rakitic and Modric were scrapping for possession, and winger Ivan Perisic, who had been a potent weapon with his driving runs, only impressed with his hairstyle.
"We expected Portugal to counter and we were playing really well for 120 minutes, controlling the match, not conceding any chances except the last one that was our mistake - and we were punished for that."