The first half saw neither team able to break the deadlock, while the second period almost mirrored the first.
However, in the 82nd minute, Oman's Mohammed Obaid al Qaidi found a way past Bahrain goalkeeper Ammar Mohamed Abbas Jaafar Ahmed to give Rasheed Jaber's boys a 1-0 lead.
But Thawadi spoiled Oman's party with a strike deep into added-on time to earn it a point.
Both teams have four points but Oman trails Bahrain on goal-difference.
Oman coach Jaber was disappointed with the result after his team had defeated the hosts 3-0 in its second match on Thursday. Jaber said, “I have really nothing to say. We were supposed to win this match easily because we had many chances. However, we only scored once. Bahrain depended on counter-attacks. It had two or three chances to score in the second half. In the additional five minutes, it scored as players lacked concentration and discipline. I am not happy with the result.”
Bahrain's coach Mohamed Ali al Muqla said, “It was difficult game, but we were relatively organised compared to the previous match. Oman had many chances to score in the second half, but it scored only once.”
Oman had begun its campaign with a 1-5 loss to UAE and now plays Nepal in its concluding match on Wednesday.
Earlier, UAE reached the summit after beating Kyrgyz Republic 4-1 on Monday. It has nine points while the hosts are second with six. Nepal is at the bottom with zero points.