The resumption of flights comes as the Southeast Asian archipelago loosens quarantine rules even as it battles a surge in Covid-19 cases fueled by the Omicron variant.
A Singapore Airlines plane carrying 109 international travelers and 47 Indonesians landed in Bali on Wednesday, the island's governor Wayan Koster told a press conference.
The foreign visitors must stay in a quarantine bubble at one of 27 designated hotels for three to seven days, depending on the number of vaccine doses received, according to new nationwide rules published on Wednesday.
"I hope that in early March, there will be no more quarantine obligation for tourists as long as they comply with health protocol requirements and show negative test results on departure and arrival," the governor said.
Arriving at Bali airport, Australian holidaymaker James said the re-opening was a "great sign" for tourism.
Swiss national Manuela, a frequent visitor to Bali before the pandemic, said she had been eagerly anticipating the first flight to the "Island of the Gods".
"Two years not going to Bali is a long time. After my friend wrote me that Bali would open, I immediately looked for the first flight," she said.
Singapore Airlines said it will operate daily flights between the city-state and Bali to meet "good demand".
Other airlines including Australia-based Jetstar Airways could resume flights to the holiday hotspot as early as next month, Bali's governor added.
"We are aware of the increasing and fluctuating Omicron variant cases, but as long as we are strictly implementing health protocols, we should not be worried," said Bali Hotel and Restaurant Association chair Rai Wijaya.
Bali authorities trialled a limited re-opening in October for a group of select countries but the response was tepid due to strict quarantine requirements and the absence of direct flights.
Indonesia reported a record number of new coronavirus cases on Tuesday.
Daily infections topped 57,000, according to the government's Covid-19 taskforce, surpassing the previous peak in July last year during the country's Delta wave.
Elsewhere in the region, the Philippines re-opened for international tourism last week while Vietnam is planning to welcome back foreign tourists from Mar 15.