Abadi ordered the strike against the jihadists "because of the danger they pose to Iraqi territory," a statement said.
A video released by the air force showed two F-16 fighter jets in action.
"These raids demonstrate the growing capacity of our armed forces to hunt down and liquidate terrorists," it added.
The US-led coalition fighting IS said the air strike targeted an area of eastern Syria's Deir Ezzor province near Hajin, around 50 kilometres (30 miles) from the border with Iraq.
The strike, carried out with intelligence support from the coalition, "demonstrates Iraq's commitment to destroy Daesh (IS) remnants who continue to threaten their citizens", said Brigadier General Robert B. Sofge, deputy commander of coalition operations.
Iraq declared victory in December against IS, which launched a sweeping offensive in 2014 and at one point controlled a third of the country.
The jihadists still control pockets of desert along the border with Syria, where Iraq had already carried out limited raids against IS before Thursday's strike.
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