Soccer's governing body ruled on Tuesday that Japanese referee Toshimitsu Yoshida made a "technical error" in disallowing an Uzbekistan penalty and then awarding Bahrain a free kick instead of ordering it to be retaken.
Uzbekistan's 1-0 home victory has been wiped out and Wednesday's second leg in Bahrain has been postponed. The tie will instead be played on October 8 and 12.
"Taking into consideration that the referee...had indeed committed a technical error, as a consequence, the match needed to be replayed," FIFA said in a statement.
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Yoshida waved off Server Djeparov's 39th-minute penalty in Tashkent and gave Bahrain an indirect free kick after spotting an infringement.
"In such a situation, the laws of the game require the referee to order the penalty kick to be retaken," said FIFA.
The decision was approved by Lennart Johansson, chairman of the 2006 World Cup organising committee.
Uzbekistan, however, are still unhappy with the verdict after FIFA rejected their request to be awarded a 3-0 win.
"Obviously it is not fair for us to replay the whole game after winning 1-0 and then being robbed of a successful penalty," Uzbekistan Football Federation (UFF) spokesman Sanjar Rizayev said.
Rizayev added that UFF officials would attend the FIFA congress in Morocco on September 10 and lobby for the game to be restarted from the penalty incident with Uzbekistan 1-0 up.
"Since FIFA did not award us a 3-0 win as we demanded, we ask for the first leg to be replayed starting in the 38th minute with that penalty being retaken," he said.
FIFA's decision came after a formal protest from the UFF following the match in Tashkent.
Yoshida refused to elaborate on his decision after the match and remained tightlipped about the row on Tuesday.
"At the moment, I'm not in a position to make a direct comment on it," Yoshida told Reuters. "I have not been contacted by the Japan Football Association so it would be wrong to say anything."
The winners of the tie will play the fourth-placed team from the CONCACAF region over two legs for a place at next year's World Cup in Germany.
Japan, South Korea, Iran and Saudi Arabia have already secured the four automatic Asian spots.
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