Egyptian judoka Islam El-Shehaby lost by Ippon to Or Sasson of Israel in the 32 round of men's 100kg event on Friday.
The game had created a lot of controversy before it even started as several voices in Egypt had demanded the withdrawal of El-Shehaby from the game to avoid engaging with an Israeli opponent.
However, president of the Judo Federation Ihab Nosseir confirmed on Thursday that El-Shehaby will contest the event.
After the defeat El-Shehaby declined to shake hands with Sasson, avoiding the latter's outstretched arm.
Judo players always bow or shake each other's hands before and after the match as a sign of respect in the Japanese martial art.
He was heavily booed by the fans present at the Carioca Arena 2.