The result means qualification for a fourth-consecutive World Cup is all but assured if the Socceroos can beat Japan on Thursday.
The Saudis took the lead after 20 minutes from the penalty spot after Mohamed Fawzi fouled Nawaf Al Abid in the box.
But they were pegged back a minute later after Tariq Hassan’s sublime cross found Ali Mabkhout who controlled the ball beautifully before rifling a volley into the bottom corner.
Not to be outdone, Ahmed Khalil danced around his opponent before launching a 30-yard screamer at the hour mark to put the UAE ahead.
The UAE were reduced to 10-men after Mahmoud Al Hammadi received a second yellow card in injury time.
But it was too late for the Saudis to fight their way back into the match.
The Emiratis will play Iraq in their final group game and still have a slim chance of qualification but need both Australia and Saudi Arabia to lose their remaining games by large margins and must win their final fixture by an equally large margin.
The Saudis will face Japan at home in their final group game.
The Socceroos will play Japan on Thursday night in Saitama and Thailand next Tuesday night at AAMI Park.