Two men with links to the Apex gang that rioted in Melbourne's CBD on the weekend have been arrested over a series of carjackings.

Special Operations Group police helped make the dramatic arrest on Monday afternoon when the heavily armoured unit swooped on the alleged offenders outside a fast food restaurant in Dandenong.

Two 18-year-old men, one from Dandenong and the other from Noble Park, were taken into custody just after 2pm on Heatherton Road in Dandenong.

Officers at the scene said the arrest was not related to the events of Saturday night, however the Apex gang is believed to have started the mass brawl near Federation Square.