The fan, Hendri Mulyadi, 25, later apologised although many online postings cheered his antics.
"I apologise to the football fans across Indonesia for what I've done," Mulyadi was quoted as telling Kompas.com after the match on Wednesday which Oman won 2-1.
He picked up the ball deep in Oman's half late in the game and showed a neat turn of pace to take it into the box but the goalkeeper blocked his effort.
A policeman, who had visibly struggled to keep up with the bare-footed fan, eventually caught up, put him in a headlock and dragged him away.
Indonesia's loss in Jakarta's national stadium in front of more than 40,000 spectators stopped the home side from reaching the final round of the Asian Cup for the first time since 1992.
"I was very disappointed with the Indonesian national team. They never win. It's either lose or draw," Mulyadi said.
Indonesian was once a powerhouse in Asian football, but the team's fortunes have been on the slide in recent years and they are firmly at the bottom of Group B with no chance of qualification.
Online postings next to footage on YouTube rallied behind Mulyadi: "Wah, he could be a future striker for Indonesia," said one posted by Crackerjos. "This guy is a hero!!!" said another.
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