The escape happened at around 2.30pm when the prisoners were out in the yard during their exercise period. A car drove up to the institution and the two men, aged 21 and 28, began to climb over the the fence.
When staff went to stop the men they were threatened, said Niclas Åkesson, duty director at the Hall and Håga prisons.
He said that the men had been jailed for several minor crimes and neither had much time remaining of their sentences.
“They would have been released at the beginning of the autumn,” said Åkesson.
A large police operation got underway in the area in an effort to track down the men, but as of Saturday evening they were still on the run.
“After a tip-off we found their clothes in Vårsta,” said Towe Hägg, spokesman for Stockholm police.
Police involved in the hunt stopped a car carrying four people on the E20 motorway. It is thought that the car could be linked to the escape and the four were taken in for questioning.
Håga is a closed facility housing 64 prisoners who are serving sentences of up to two years. The majority have been found guilty of drugs-related offences.