The woman was the only one working when two men entered Crofters Bar about 11pm.
Manager Sukhvinder Singh said the woman was powerless when they pointed a gun at her and told her to hand over all the money, including what was in the safe.
Mr Singh declined to say how much was stolen, but said it housed a lot of coins, notes and three cash drawers from tills which had been closed for the night — all of which was taken.
About 20 customers were at the Gordon Rd establishment at the time, but many were outdoors and unaware of the situation, he said.
Mr Singh was dropping locals home in his car when the robbery occurred and returned just after the pair had fled.
The bartender was already on the phone with police when he arrived and officers were at the scene within five minutes.
Mr Singh had supplied security camera footage to the police, which showed the two young men entering the bar wearing masks.
One carried a gun, but it was hard to tell what type it was.
Mosgiel was a small community and people would want to see justice served, he said.
He believed it would be a while until people felt safe at the bar again.
The robbery also impeded trading, as Saturday was its busiest day, and police were busy investigating the scene until the afternoon.
The adjoined Big Barrel liquor store, owned by the same parent company, was also closed Saturday.
A police spokeswoman said they were investigating the incident and nobody was injured.
In 2016 the former owner of the bar was robbed at knifepoint while closing up, with about $13,000 stolen.
Mosgiel-Taieri Community Board chairwoman Joy Davis said the incident was distressing for those involved, but she had every confidence in police.
She urged anyone with any information to share it with investigators to help bring the incident to a speedy resolution.
While there was not enough information to make comments about the perpetrators, she hoped that if they did need help they would reach out and get it, Ms Davis said.
Additional reporting Oscar Francis
