After eight years with the paper, and more recently AFR Weekend, Mr Latham told editor in chief Michael Stutchbury on Sunday that he had written his last column for the masthead.
Mr Latham had taken aim at Australian of the Year and domestic violence survivor Rosie Batty and has also made transphobic comments about Group Captain Catherine McGregor, Australia's most senior serving transgender military officer in his AFR column.
"Australia's highest-profile soldier is The Artist Formerly Known As Malcolm McGregor – a military adviser with a direct line to the Prime Minister. He/she penned the infamous YouTube broadcast that lifted the lid on sex abuse and alcoholism in the Australian army – again, not the sort of thing the Iraqis want to hear," Latham wrote.
"Mark has been a provocative and highly readable columnist for the Financial Review," Mr Stutchbury said.
"He has been both loved and hated by readers, sometimes by the same ones at different times. While I didn't agree with everything Mark wrote, he has played a significant role in Australian public life and brought rare personal insight into his writing."
A Twitter account called @RealMarkLatham has been accused of trolling prominent women online, but it is not clear if the account is connected to Mark Latham.
Buzzfeed has linked the account to Mr Latham, however the person behind the account has denied it.
The person behind the Twitter account dismissed the resignation line from the AFR.
"The Dismissal: The AFR has sacked poor Latho, who has retired to Mt Hunter Lodge for a rump steak (medium-rare). Maintain The Page," @RealMarkLatham tweeted shortly before the AFR announced Mr Latham's resignation.
Earlier, the account tweeted: "Sucked in Buzzfeed wanker. Cite (sic) run by me, Mitch Carter, legend, of Monks Lane, Mount Hunter, Lathos mate from school. HaHaHaHa dickheads."
