The men were stopped in a vehicle shortly after the night's first car burning began, according to local newspaper Sydsvenskan.
The arrest follows the apprehension of another man on Saturday suspected to be behind a separate vehicle fire in the city.
Car-burning activity in Malmö seemed to calm down on Monday after some of the worst nights yet in the spate of blazes took place last weekend.
“It has been quiet. There was a car fire in Burlöv around 1am, but otherwise there hasn't been much after midnight,” Mikael Lundh, duty officer at Southern Sweden Police, told news agency TT.
At the weekend by contrast as many as 32 cars were set alight. Police suspect that sudden burst may have been a response to the recent arrests of individuals linked to serious crimes in the city.
“We can't rule out the possibility that this is a reaction to our activities in terms of crime here,” Malmö Police press officer Lars Förstell told TT.
According to police, the fires do not appear to be directed towards any particular individual, and they suspect that a small group of young men working as lackeys for hardened criminals are behind them.
Authorities in the city last month brought in a drone to monitor activity in the areas hit by the spate of burnings. Its small size and stealth make it difficult for car-burners to spot, and a handful of arrests have followed its introduction.