Police had been looking for Mr Arnada, who ignored orders to surrender after being sentenced to two years in jail for indecency in August.
He had first been tried in 2007 and cleared of all charges.
Islamist groups forced Indonesian Playboy to close down after only a few issues in 2006.
The Islamist Defenders Front (FPI), a hardline Muslim group in Indonesia, had said Mr Arnada was a "moral terrorist", and the group criticised the authorities for failing to track him down.
South Jakarta chief prosecutor Mohammed Yusuf said Mr Arnada had ignored three orders to turn himself in.
"We picked him up from Bali today to fly him to Jakarta", Mr Yusuf said on Saturday.
Mr Arnada's acquittal in 2007 was seen as a victory of freedom of the press in Indonesia, the world's most populous Muslim nation where Islamist extremists launched violent protests when the magazine appeared in 2006.
But the FPI and other Islamist groups lodged an appeal with the Supreme Court, which found him guilty of public indecency after publishing a handful of issues of Indonesian Playboy, which contained no nudity.
"We are being forced to act by the FPI as a plaintiff in this case", Mr Yusuf said on Saturday.
The Indonesian parliament passed a controversial anti-pornography law in 2008, which was backed by Islamist groups.
But the law also prompted protests across Indonesia, particularly on the predominantly Hindu island of Bali - a favourite destination for tourists.

Harrison Ballantyne was found near a bridle-path close to Daventry International Rail Freight Depot at 17:20 BST on Tuesday.
The 11-year-old with the "cheeky smile" was with four other boys at the time.
His parents said he was "an outgoing boy and loved to be active outside, exploring, climbing and getting muddy".
Harrison, who came from Crick, was pronounced dead at the scene.
One of his companions was taken to hospital but was uninjured.
Police said the Guilsborough Academy pupil came into contact with electricity from an overhead line.
His parents, who have not been named, said: "In less than 12 years he filled our lives with happiness. His lively character lit up the room.
"His innocence and inquisitive nature led him to the railway track, stealing him from this world so soon after he arrived.
"We will struggle to live without him."
British Transport Police is continuing to make enquiries into the circumstances of his death, but is not treating it as suspicious.
Supt Chris Hodgkiss said: "His friends who were at the scene have all now been spoken to and offered support, as have pupils at his school."
"We cannot stress enough the dangers of the railway," he added.
Officers are patrolling the area to keep children away.
Julie Swales, principal of Guilsborough Academy, said Harrison was an "enthusiastic student" and "a natural leader in and out of class; he will be greatly missed by all of us".
The school has opened a book of condolence and a fundraising page has been set-up to raise money for a memorial to Harrison attracting almost Â£5,000.
The former editor of Indonesian Playboy, Erwin Arnada, has been arrested on the island of Bali.
[NEXT_CONCEPT]
The parents of a boy who was electrocuted near a rail depot have paid tribute to their "kind and thoughtful" son.