The prestigious cup tie went to extra-time with both teams level at 1-1.
But four minutes into the additional alotted time, Clattenburg brought the game to a standstill because of the calls to prayer echoing from nearby mosques surrounding the King Salman Sports City stadium.
The former Premier League match official resumed play three minutes later.
In the 118th minute, Sami Al Khaibari scored a winner for the hosts as they advanced to the semi-finals.
It was announced in February 2017 that Clattenburg would leave his Premier League post for a job in Saudi Arabia, and he reffed his final game in April – a 1-0 win for Leicester at West Brom.
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