The Australian-hosted tournament started just as the US and Israel launched air strikes on Iran, killing Supreme Leader Ali Khamenei.
After the team opted to stand in silence during Iran's anthem before their first match against South Korea, they were labelled as "wartime traitors" by state TV presenter Mohammad Reza Shahbazi.
In a statement posted by Iran's football federation (FFIRI) on its Telegram page on Friday, which has since been deleted, Jafari said: "Our girls were affected in the first match by the heavy atmosphere that had been created...
"But the greater mistake was made by those who, at home, failed to understand that atmosphere and sounded the call to arms against the daughters of this land," she added, referring to the presenter's comments.
"What I have asked of the federation is to pursue the matter, because it affected our players psychologically, and we suffered the consequences.
"I am certain that if that atmosphere had not been created, not a single one of our players would have stayed in Australia."
Australia this week granted humanitarian visas to five Iranian players who sought asylum during the tournament. Two more squad members were granted asylum on Wednesday, and one decided to return to Iran.
"Australian police called the players in several stages and sat down with them one-on-one to persuade them to stay, influenced by the political atmosphere that had arisen," Jafari said.
"Fortunately, the majority of the team members responded negatively. Even Mohaddeseh Zolfi, who had responded positively, soon changed her mind and, God willing, will come to Iran with the team."
"The rumours about Golnoosh Khosravi and Afsaneh Chatrenoor are also not true at all, and they are now with us in Malaysia and we will be leaving for Iran soon."
