The result moved Saudi Arabia to six points at the top of Group F while Thailand are two points behind in second after they drew 0-0 with Oman (one point) earlier on Sunday. Kyrgyzstan are bottom after losing both their games.
Kyrgyzstan had Aizar Akmatov and Kimi Merk sent off early in each half and the red cards set the tone for the rest of the match as Saudi Arabia finished the game with 28 shots while facing only one.
"The two red cards were correct. You have to play football and not kick (the opponents). We would have preferred to play 11 versus 11," Saudi Arabia coach Roberto Mancini told reporters.
"We missed many chances to score today. But if we score two goals every game then I'm happy. I'm happy with my players."
Kyrgyzstan had a nightmare start to the game when centre-back Akmatov saw red in the ninth minute for a high boot on Sami Al-Naji's shin as the midfielder drove towards the box.
The Kyrgyz defender was initially cautioned but received a straight red after VAR intervened and the referee watched the replay.
Saudi Arabia took time to make their possession and man advantage count but after several opportunities to open the scoring, they finally made the breakthrough in the 35th minute when Mohamed Kanno turned in a cross at the far post.
Kyrgyzstan's night went from bad to worse when Merk was sent off in the 52nd minute for a reckless challenge on Hassan Tambakti where he caught the defender on the ankle, with VAR intervening again after the midfielder was only cautioned.
Kyrgyzstan went into damage control and played at times with six players in the backline to thwart wave after wave of Saudi attacks and they managed to hold firm against Mancini's side while goalkeeper Erzhan Tokotayev made many crucial saves.
But Faisal Al Ghamdi doubled their lead with a long-range strike that slipped through the gloves of Tokotayev in the 84th minute, leaving him crestfallen on the turf.
"What do I say? To play against Saudi Arabia is difficult. After the second red, it was just a question of the score," Kyrgyzstan coach Stefan Tarkovic said.
"It was very bad receiving two red cards. From my perspective we showed spirit, they fought for the result, for their country. They fought till the end."
