The fire on Saturday “completely destroyed” the church in the Lignon residential zone of the municipality of Vernier, cantonal police said
One person suffered smoke inhalation from the blaze that broke out shortly after noon, police said.
Around 50 emergency services workers responded to the fire.
An investigation into the incident rapidly led to the two children being implicated as suspects, police said.
The force did not say exactly how old the children were.
But it said said given their young age, they will not be held criminally responsible.
Investigators interviewed the pair in the presence of their parents before letting them return home.
The investigation into the cause of the fire continues.
The destruction of the church forced the congregation to use a nearby protestant church for Sunday services.
Le Lignon is a massive housing project built by the canton of Geneva between 1963 and 1971 with 2,780 apartments in large building blocks, including two towers of 26 and 30 storeys respectively.