A video of Flicker's defiance had social media users praising the athlete and blasting the "racist" organisers.
"Israel is my country, and I'm proud to be Israeli," Flicker told Israeli Channel 2 news after the event.
"The anthem that they played of the world federation was just background noise. I was singing HaTikvah from my heart.
"I'm proud of my country. The whole world knows that we're from Israel, knows who we represent. The fact that they hid our flag, it's just a patch on our flag."
A number of Islamic countries in the Arab League - including the United Arab Emirates -
do not recognise the State of Israel, and continue to boycott it diplomatically and economically.
According to the Daily Mail, Israeli athletes have suffered a series of similar discriminating acts at high profile sporting events. These include at last year's Rio Olympics when Egyptian Judoka athlete Islam El Shehaby refused to shake hands with an Israeli star who beat him.
The IJF had earlier sent a letter to the UAE Judo Federation demanding that "all delegations, including the Israeli delegation, shall be treated absolutely equally in all aspects, without any exception", AP reported.
Israel's Sports and Culture Minister Miri Regev told the Daily Mail it was of "utmost importance" that her country's athletes display the flag and sing the national anthem at international competitions and insisted that boycotting the competition would "only play into the hands of those refusing to recognize our existence".