The accident occurred around 3:40am (0240 GMT) near the town of Drazevac - some 220 kilometres (137 miles) from Belgrade - on the highway linking Bulgaria and Greece to northern and western Europe.
"Two Afghan nationals were killed and 10 others injured... when their car ... hit a protection fence," police said in a statement.
Authorities said it was unclear who was driving the vehicle, adding there was an "intensive" search underway.
Serbia shuts borders for Pakistani migrants
Serbian national broadcaster RTS reported that all the injured, including five children, were transferred to a hospital in the nearby town of Nis.
The migrants had "extremely severe head and limbs injuries... we are doing everything to save their lives," doctor Miodrag Lazic from the Nis hospital told RTS.
The report quoted a migrant as saying he travelled from Iraq with his family, including two children, and that the driver had driven very fast and ignored their appeals to slow down.
Adil Gilani tipped to become envoy to Serbia
Serbia lies on the so-called Balkan route taken by hundreds of thousands of migrants from the Middle East, Asia and Africa since mid-2015 on their way to western Europe.
The route was effectively shut down in March, but migrants have continued to cross the region in smaller numbers often with the help of traffickers.
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