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."
Unsurprisingly, given that Indonesian football is already treading on eggshells with FIFA over the chaotic state of its domestic game, the PSSI quickly accepted the punishment.
FIFA has also ordered Santoso to pay a fine of 6,000 Swiss francs on top of his touchline ban.
Indonesia had their goalkeeper sent off after two minutes while Bahrain were awarded four penalty kicks in a match which prompted FIFA to launch an investigation.
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.
Indonesia, already eliminated, fielded a vastly inexperienced side after being blocked from selecting their regular squad by the PSSI because many play in the rebel Indonesian Super League.
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.