The men entered the building through a back window and were armed with a gun and crowbar.
Employees were able to raise the alarm while the robbery at the check-in desk was ongoing.
The pair escaped in a stolen car and opened fire when a police chase ensued. No one was injured in the incident.
Police eventually lost trace of the vehicle, which was later found abandoned south of the city in Örnsberg.
One of the suspects was arrested in a nearby building but the search for his accomplice continues. A further person was taken in for questioning by police on Friday and later released.
A weapon and a bag of money were found in a forest area close to the stolen vehicle.
No passengers were believed to have noticed the robbery but a number of Viking Line employees received counselling advice from the Red Cross after the incident.
The robbery resulted in delays to ferry traffic on Friday but no routes had to be cancelled.