The youths, aged 16 and 14, were arrested today on suspicion of arson at the Baitul Futuh Mosque in Morden.
The blaze at the mosque was tackled by 70 firefighters yesterday.
An administration building was badly damaged but not the mosque, London Fire Brigade said.
A man was taken to hospital suffering from the effects of smoke inhalation and about 30 others left when the alarm was raised.
The 5.2 acre (2.1 hectare) mosque serves the Ahmadiyya Muslim Community and there is space for at least 10,500 worshippers, according to its website.
"The fire was contained to the hall at the front of the building and some adjacent offices. We are extremely grateful for the support of the local community and leaders."
The two arrested teenagers remain in police custody at a south London police station.