The head of the statue had been removed but was eventually found
The statue was erected after the Second World War, in 1950.
The two young men could face up to two years of imprisonment.
Riots led to the torching of a basement nursery at the historic church, also known as the "church of the presidents".
Alleged racism continues to be used as a pretext to attack Christian symbols throughout the West.
Father Junipero Serra was beatified in 1988 by Pope John Paul II and canonised by Pope Francis in 2015.
As BLM protests spread all over the West, several historical statues have been vandalised in Belgium in the last weeks.
Attacks on religious freedom have been growing continuously since 2014 when the OLRC began collecting data.
Churches in France are being vandalised on a weekly basis.