Saudi Arabia, who beat China in their opening match of the campaign, opened up a three-point cushion at the top of Group C.
The top two teams from each of the five qualifying groups and the best third-placed team will join defending champions Japan, hosts Australia, South Korea and North Korea in March 2015 for the next edition of the tournament.
Cheered on by about 75,000 home supporters at the Gelora Bung Karno Stadium in Jakarta, Indonesia took a surprise lead through captain Boaz Solossa in the fifth minute as they looked for their first ever win over the Saudis.
A defensive error meant Solossa collected the ball at the edge of the box and he made no mistake by curling in a left-footer to stun the three-time Asian Cup winners.
Al Salem restored parity 10 minutes later, deftly heading in a cross from Nawaf Al Abid from the right flank to beat the goalkeeper at the near post.
Saudi Arabia dominated the match from there on but Indonesia held firm and it was not until the 56th minute that Al Salem outjumped the defenders to head in another cross for the winner.
With the match mostly played under torrential rainfall, Juan Ramon Lopez Caro, who replaced Frank Rijkaard as coach after Saudi Arabia flopped at the Gulf Cup of Nations in January, was happy with his team's performance under pressure.
"We faced a strong team with an organised defence so we had to try to score from every angle," the Spaniard told the Asian Football Confederation website (www.the-afc.com).
"Indonesia's goal surprised us but we kept our composure and we turned the tables. The group is very strong and very competitive. We should keep our feet on the ground and focus on our next match."
Indonesia managed to avoid a FIFA ban after rival soccer leagues agreed to merge last Sunday after a long running wrangle.
The national team's caretaker coach Rahmad Darmawan blamed his players' lack of international exposure for the loss.
"Although we scored an early goal, the players played nervously in the first half but they overcame their nerves in the second half and played better," he said. "But it was too late and we paid the price for our nervousness.
"I think we still have a chance to qualify but we need more international friendlies to warm-up for these type of games. So whoever will be at the helm for the next match needs to ask the federation to set up more friendly matches."
In other Asian Cup qualifiers late on Friday, Bahrain beat Qatar 1-0 to take a three-point lead at the top of Group D while Lebanon beat Thailand 5-2 at home in Group B for their first win of the campaign.
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