Police said the blast occurred at around 7am outside the Orthodox church of Agios Dionysios in the upmarket Kolonaki area of the capital, ahead of a Christmas holiday service to mark St Stephen's day.
The two victims were taken to hospital.
Neither of the two men suffered injuries that are life-threatening, according to police and church officials.
Fr Symeon Voliotis, an aide at the archbishop's office, told state-run ERT television that the caretaker found the explosive device at the front entrance of the church, moved it and alerted police.
"Any action that threatens life or disturbs the peace must be condemned," he said.
"My first thought was that someone homeless may have been hurt, because they often seek shelter there. But fortunately that was not the case."
Authorities are already on alert following an attack on the private Skai television station when a powerful bomb damaged the front of the building on December 17.
Militant far-left and anarchist groups have carried out attacks over the Christmas holidays in recent years.
Anti-terrorism division officers are leading the investigation into the explosion, and officers cordoned off the busy central Athens area while colleagues gathered evidence.
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