Police officials at the scene "confirmed it was the imam" who died when a firebomb was thrown into the Shiite mosque, police spokeswoman Marie Verbeke said.
The imam, who succumbed to the fumes in the burnt-out place of worship, was with a second person, who was lightly injured, at the time of the attack.
"A suspect was taken into custody at the scene," Verbeke added.
A witness saw the suspect, a man, set fire to the building, Verbeke said, but no other details were immediately available.
Anderlecht Mayor Vincent Van Goidsenhoven said the suspect threw a Molotov cocktail at the mosque, Belga news agency reported.
"The mosque was apparently almost entirely burned down," Verbeke said.
Belgian public broadcasters RTBF and a stream of Twitter users said that a group of at least 50 people had gathered outside the Shiite mosque.
Police said they received a call at 6:45 pm (1745 GMT) and the body was pulled out 45 minutes later.
The area around the mosque, near Belgium's main international railway hub, has a large immigrant Muslim population.
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