The airport at Denpasar was reopened on Thursday about 2.30pm local time. However, the risk from the ash cloud was still too high for flights to and from Australia to depart until possibly the weekend or next week, Jetstar said.
Jetstar spokesman Phil Boeyen said thousands of travellers would have been affected.
The airline cancelled 22 flights between Australia and Denpasar today, following the cancellation of another 16 flights on Thursday.
No Jetstar planes have flown to Bali since Tuesday because the ash cloud was too close to safely fly, he said.
An update on whether Saturday's flights will get off the ground is expected today.
"We started cancelling on Tuesday ... we haven't had any flights go since [then]," Mr Boeyen said.
"So far, it's certainly been thousands of travellers affected."
Jetstar has posted a travel alert on its website about the disruptions, which said affected passengers can rebook their flights within one month or opt for travel vouchers.
"While we regret the frustration these cancellations will cause, the safety of our customers and crew is always our first priority," Jetstar said.
"We'll continue to monitor the movement of the volcanic ash cloud from Mt Rinjani in Lombok, Indonesia and will resume flying as soon as we deem it safe to do so."
An Air New Zealand spokeswoman said any passengers wishing to fly with the airline to Bali would get a direct flight to Australia and then change airline.
"Our direct flights to Bali operate seasonally ... we don't actually have any disruptions because we're not operating directly at the moment."
Virgin Australia cancelled 12 flights to and from Bali on Thursday, and another 13 on Friday and Saturday.
It has also posted a message to customers on its website, stating they can rebook their flights within a month or receive a full travel credit for their disrupted flights.
"...our team of meteorologists and the Volcanic Ash Advisory Centre have advised that conditions in the vicinity of Denpasar Airport remain unsafe for flying.
"We continue to monitor the situation closely," Virgin said.
Bali airport management had to spend several hours cleaning the runway and aircraft of ash before any flights could take off or arrive on Thursday, AAP reported.