Santoso was sent to the stands by Lebanese referee Andre El Haddad after the fourth official indicated that the coach had asked if there was "money involved" in the game in Manama.
"I accept the punishment and I regret my behaviour," Santoso told the Jakarta Globe. "I was just saying to the fourth official 'Is there money involved in this match?'"
The 42-year-old, now in charge of the under-23 side, added: "I won't mind if the PSSI [Indonesia's FA] decides not to appeal it."
Bahrain had needed to win the Group E game by a nine-goal margin to have any hope of advancing to the final round of Asian 2014 World Cup qualifiers. Qatar's 2-2 in Iran dashed those hopes.
The country is still flirting with a FIFA ban for failing to reconcile the country's two leagues, having already wriggled out of an earlier deadline last month.
The embattled PSSI, already facing threats from Indonesia's government vowing to take control, has until June 15 to get its house in order of suffer FIFA sanctions.
