The incident has occurred in the northwestern city of Saraqeb in Aleppo Province, where a court formed by the militants issued a verdict to flog the men for what they claimed was violation of marriage traditions.
The two were whipped for acting against the way the militants carry out the marriage procedure.
The al-Qaeda-affiliated Salafi militants in Syria have conducted similar acts in over two years of turmoil in the country.
Syria has been struggling with s Western-backed insurgency since March 2011which has left many people dead and forced many to leave the country to escape the war.
Syrian government says the bloody chaos is being charged from outside the country while the US, Israel, Qatar and some of their allies have been supporting the insurgents to topple the legitimate government of Bashar Assad.
A recent report by the Financial Times revealed that the Qatari government has spent some three billion dollars in the past two years to support the anti-government groups in Syria, which far exceeds what provided by any other government.