A Pakistani national was also released, the Qatari foreign ministry said.
The pair, who have not been named, were among more than 20 people abducted from a desert hunting party close to the Saudi border last December.
"Efforts are still ongoing to free the rest of the 26 kidnapped," a brief statement published on Qatar's official QNA news agency said.
It was unclear if any other Qatari royals were still being held.
Faleh al-Zayadi, the governor of Muthanna province where the hunters were seized, told AFP at the time that "a number of members" of the Qatari ruling family were among those abducted.
He said the kidnappers were heavily armed and travelled in dozens of vehicles.
A foreign ministry spokesman told AFP that negotiations were continuing with the Iraqi government to try to secure the release of the remaining abductees.
It is not known if any ransom was paid for the two men who were freed.
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The hunters were abducted when gunmen attacked their camp in a Shiite-majority area of southern Iraq.
Nine members of the party managed to escape and cross into nearby Kuwait.
Earlier this year, the Doha government said Baghdad had a "responsibility" to free all those who had been kidnapped.
Pressure has also been placed on Iraq by the Gulf Cooperation Council, of which Qatar is a member.
In a joint statement immediately after the kidnapping, the GCC said Iraq should take "decisive and immediate measures" to secure the release of the hunters.
There is widespread enmity towards the Gulf Arab states in Shiite areas of southern and central Iraq because of their support for Sunni rebels in the conflict raging in neighbouring Syria.
Iran-backed Shiite militias, which have a major presence in the region, have sent fighters to Syria to support President Bashar al-Assad's regime.
The hunting party was in Iraq on an officially licensed expedition and Doha has put pressure on the Shiite-led government in Baghdad to help secure the hostages' release.
Wealthy Gulf Arabs often brave the risks of travel to countries like Afghanistan and Pakistan as well as Iraq to hunt with falcons without the bag limits and conservation measures they face at home.
Their favoured prey is the houbara bustard, a large game bird once nearly hunted to extinction in the Middle East.