The men suffered fatal injuries after trees fell on them.
Within a space of 30 minutes, the heavy storm wreaked havoc across the city, ripping off roofs and roof tiles, knocking down chimneys, uprooting trees and flooding the streets.
Speaking to reporters at the scene, Mayor Tomislav Tomašević said that 85 per cent of tram services were out of service and that workers from the ZET municipal transport company would be in the field all through the night to restore transport services.
Gale-force winds also battered Krapina-Zagorje, Varaždin and Međimurje counties in northern Croatia, felling trees, damaging properties and causing power cuts.