The pair, said to be from North Africa, first came to the attention of officials when a car, believed to have been driven by them, sped past traffic police on Rome’s ring road on Sunday night, Corriere reported.
The car was later found abandoned, with two guns inside.
Police then traced the owner of the car, which led them to an apartment in Infernetto, a hamlet between Rome and Ostia.
There they found the extremist group’s black flag, and a map of Rome with various locations encircled.
The discovery comes less than a month after Isis published a photo of its flag superimposed on the obelisk in St Peter’s square on the front cover of its propaganda magazine, ‘Dabiq’.
The magazine contained an article about the fight against "Rome" and "the Romans", terminology used to refer more widely to the West.
The magazine, which is published in several different European languages, is used by the organization to radicalize and recruit young people around the world, especially in the West.
Italy stepped up security in September following threats from the group, with Interior Minister Angelino Alfano saying that the threat posed by Isis is equal to that of terrorist organization al-Qaeda after the September 11th attacks against the US in 2001.