Haffajee, 36, who was a trainee at the newspaper in 1991, will take over from Mondli Makhanya, who will take up the post of editor at the Sunday Times in February.Haffajee told the Mail & Guardian Online on Thursday that she had her eye on the job for some time.
It focuses on political analysis, investigative reporting, Southern African news, local arts, music and popular culture.
The publication was started as an alternative newspaper by a group of journalists in 1985 after the closure of two leading liberal newspapers, The Rand Daily Mail and Sunday Express.
It was originally known as the Weekly Mail, as the paper did not have enough money to publish daily.
Weekly Mail was one of the first newspapers to use Apple Mac desktop publishing. The paper was renamed the Weekly Mail & Guardian from 30 July 1993.
The Weekly Mail criticised the government and its apartheid policies, which led to the paper's suspension in 1988 by then State President P. The London-based Guardian Media Group (GMG), publishers of The Guardian, became the majority shareholder of the print edition in 1995, and the name was changed to Mail & Guardian.
In 2002, 87.5% of the company was sold to the Newtrust Company Botswana Limited, which was owned by Trevor Ncube, a Zimbabwean publisher and entrepreneur.In 2006 MD Africa became the Mail & Guardian's national distributor.The change resulted in good circulation growth, despite difficult market conditions.In 2013 the newspaper achieved a record period with 51 551 copies circulated.MDA distributes a number of publications including Noseweek and Destiny magazine.However, by the first quarter of 2015, distribution had collapsed to 30,714.