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.
The former editor of Indonesian Playboy, Erwin Arnada, has been arrested on the island of Bali.