The Southeast Asian country has seen a jump in cases, with more than 36,000 cases recorded on Sunday and the bed occupancy rate at hospitals in the capital reaching 63 percent.
The move to bar tourists flying to Jakarta comes just days after Bali welcomed its first direct international flight in nearly two years.
The new regulations apply to foreign tourists and Indonesians who have travelled overseas for holidays, the Indonesian transport ministry said in a statement released late on Sunday.
The decision to “temporarily restrict tourist arrivals” was intended to slow the spread of the coronavirus, said Novie Riyanto, director-general for civil aviation at the ministry.
Tourists flying from overseas will still be able to arrive at Bali airport, as well as at Batam and Tanjung Pinang in the Riau Islands near Singapore.
Police have also implemented a curfew in the centre of Jakarta from midnight to 4am.
Indonesian officials have warned that the surge in cases driven by Omicron may not peak until late February.
Despite these concerns, the resort island of Bali welcomed a flight from Tokyo last Thursday carrying six foreigners, mostly travel agents who were on board to monitor the island’s readiness to receive foreign tourists.