He is alleged to have "misled the court" during the drugs trial, the Crown Prosecution Service (CPS) said.
Mr Mahmood said in a statement that he denied the offence and would "vigorously contest it at court".
He has been charged alongside Alan Smith, who was his driver.
Former News of the World reporter Mr Mahmood, who often posed as a sheikh during his investigations, claims to have helped put more than 100 criminals behind bars during his 25-year career.
Nick Vamos, of the CPS, said: "After carefully considering all of the evidence the CPS has decided that there is sufficient evidence for a realistic prospect of conviction and it is in the public interest to charge both men.
"This decision comes after it was alleged that Mr Smith agreed with Mr Mahmood to change his statement to police as part of a trial in July 2014, and that Mr Mahmood then misled the court."
Former N-Dubz singer Miss Contostavlos, 27, had gone on trial at Southwark Crown Court charged with supplying a class A drug, which she denied, after it was alleged she had brokered a cocaine deal.
It had featured in a Sun on Sunday story in June 2013, following an investigation by Mr Mahmood.
A judge threw out the case last July and also cleared Miss Contostavlos's friend Michael Coombs, known as Mike GLC.
Following the collapse of the trial, she said she had "never dealt drugs" and "never been involved in taking or dealing cocaine".
In a statement issued by his lawyers, Mr Mahmood said: "I am deeply disappointed that, after a totally unjustified delay, the Crown Prosecution Service have today informed me that they have decided to charge me with conspiracy to pervert the course of justice.
"I deny the offence. I will vigorously contest it at court. In the meantime I have nothing further to say."
Mr Mahmood and Mr Smith will appear at Westminster Magistrates' Court on 30 October.
Undercover reporter Mazher Mahmood, known as the "fake sheikh", has been charged with conspiring to pervert the course of justice over the collapsed trial of singer Tulisa Contostavlos.