With the score tied at 1-1, Al Bulayhi scored with a close-range header from a set piece and although the linesman's flag immediately went up for offside, VAR awarded Roberto Mancini's side the goal.
The victory takes Saudi Arabia level on three points with Thailand, who beat Kyrgyzstan 2-0 in the other Group F encounter earlier in the day when Supachai Chaided scored either side of half time.
Oman's opener in the 14th minute came against the run of play when the Saudis took a poor corner and as their opponents countered at speed, defender Hassan Tambakti clipped Muhsen Al Ghassani just as he entered the box.
The penalty was awarded after a VAR review and Salaah Al Yahyaei stepped up to score with a confident finish down the middle to draw a massive roar that echoed inside the cavernous arena.
Oman were disciplined in defence and Saudi Arabia found it difficult to break through the wall of red shirts while on the odd occasion they did get through, they wasted their opportunities with shots that did not find the target.
Mancini cut a frustrated figure near his dugout but his half time team talk must have struck a chord as his players came out with renewed vigour in search of an equaliser.
Oman were restricted to counter-attacks with Al-Yahyaei leading the charge and creating chances but he did not have support in the final third as they spurned golden opportunities to score a second.
Al-Yahyaei was toying with the Saudi defence in the second half but the 25-year-old had nothing left in the tank by the 75th minute, signalling to the bench to take him off and he left the pitch to rapturous applause from the Oman fans.
But Saudi Arabia were the better side in the second half and after missing a couple of chances, Abdulrahman Ghareeb took it upon himself to dribble past four Oman defenders before finishing calmly to get the Saudis singing again.
And once Al Bulayhi completed the comeback, following a period of confusion, the green corner of the stadium erupted when their players celebrated while Oman were left to wonder what could have been.
