Ten fire engines and around 70 firefighters were called to a blaze at the property on Spout Hill in Croydon, which was previously owned by comedian Ronnie Corbett.
The incident is being treated as suspicious, the Metropolitan Police said.
Four different neighbours confirmed the house was owned by Williams but had been empty for some time.
One said he bought the property four years ago from Corbett, who died in 2016.
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It comes after the singer, 32, was cleared on May 28 by a jury of raping a woman in his hotel room following a solo concert.
Jurors at Wolverhampton Crown Court deliberated for around two hours before unanimously acquitting Williams, who told the jury he had consensual sex with the woman in the city in December 2016.
Part of the first and second floor of the detached three-storey building were damaged by fire and a small part of the roof was also damaged, the London Fire Brigade said.
A statement said: "The Brigade was called at 1627 and the fire was under control by 1858.
"Fire crews from Addington, Croydon, Biggin Hill, Purley, Orpington, Woodside, Bromley and Wallington fire stations were at the scene.
"The cause of the fire is under investigation by the Brigade and Metropolitan Police Service."
There were no reported injuries and have been no arrests.
One neighbour, who did not want to be identified, told the Press Association he had seen the smoke from the blaze, adding: "We had heard it was owned by the JLS star.
"A policeman told me squatters had moved in recently. I'm not sure for how long.
"It's a bit of a shock really, seeing all of this. I couldn't say how long they were in there.
"I just saw all the smoke at about half past seven. We had been down to Eastbourne but we had trouble getting the road here because of all the engines."
The Metropolitan Police said: "At this stage, the incident is being treated as suspicious. The cause of the fire is under investigation.
"Enquiries continue, led by the South Area Command Unit CID."