Croatia head coach Ante Cacic said the best team lost after the last-gasp Euro 2016 defeat to Portugal on Saturday.
However, Portugal snatched victory in the 117th minute when Danijel Subasic palmed Ronaldo's shot into Quaresma's path to head home.
Cacic refuted suggestions his side had crumbled under the pressure of being classed as favourites after beating defending champions Spain on Tuesday to top Group D.
"We cannot say football is fair, we had many chances, we dominated for the whole match, so it was not a psychological problem," said Cacic. "The best team doesn't always win and that happened tonight."
Portugal now face Poland in the quarter-finals in Marseille and Cacic admitted he knew Croatia had missed out on a wonderful chance to go far in the competition after landing on the opposite half of the draw to traditional giants Germany, France, Spain, Italy and England.
"Of course I am really sad, we had a great chance, the draw was perfect for us," he added.
"We knew we had a really open part of the draw against Poland, but that is tournament football. Portugal are a really strong team, I congratulate my players for their effort.
"I am sure Portugal are a high quality team with some experienced players and I think Portugal are the favourites now (to reach the final)."