The poor performance of the Merah Putih when competing in the 2014 World Cup qualifier made them abandoned by several supporters who are reluctant to come to the stadium.
Indonesia fans were reluctant to attend the game, following the national team's poor third round campaign where they had lost all four matches heading into Tuesday's clash.
However, Queiroz, who initially had feared a parochial home crowd in Jakarta, said the fans should remain loyal whether their team's wins or loses.
"We still have to respect the decision of the fans who were not happy with the performance of the Indonesian team. And today this was case here," Queiroz told reporters.
"I have experienced something like this, I coached a team that loses and fans do not come to the stadium. It happens to every coach in every country."
However, the Portuguese added: "In my opinion, the Indonesian supporters were selfish. They should continued to give support, both if the national team is good or bad."
The former Real Madrid and Portugal coach still offered advice to the Indonesia fans too.
"I did not agree with this case. I convey a message to Indonesian fans, support the team when winning or losing, because the players want to show the best for them. This attitude should not happen," he said.
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