Khalil scored the winner in the 60th minute after Ali Mabkhout had cancelled out Nawaf Al Abed's 20th minute penalty for Saudi Arabia to keep the UAE's own slim chances of qualifying for Russia 2018 still intact.
Saudi Arabia remain in second place in group B of Asia's qualifying tournament with 16 points, one fewer than leaders Japan and level with Australia. Japan and Australia meet at Saitama Stadium outside Tokyo on Thursday.
The top two teams in each of Asia's two qualifying groups progress to the finals, with the third placed teams entering a series of playoffs.
The win takes the UAE on to 13 points with only one game remaining, with Edgardo Bauza's side needing to win against Iraq in the Jordanian capital Amman on Sept. 5 to have any hope of securing a second World Cup appearance in the country's history.
Al Abed put the Saudis in front from the penalty spot in the 20th minute after he had been hauled down by Mohammed Fawzi, but Mabkhout levelled the score less than a minute later with a fine effort on the turn.
Saudi Arabia's Osama Hawsawi hit the crossbar shortly after half-time, only for former Asian Player of the Year Khalil to score the winner on the hour mark.
Mahmoud Khamis of the UAE was sent off for a second bookable offence in the dying seconds of the game but the home side held on to take all three points.
(Reporting by Michael Church in Hong Kong; Editing by Christian Radnedge)
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