Koci Selamaj, 36, has been accused of killing Ms Nessa, 28.
She was found dead in Cator Park, close to her Kidbrooke home, the day after she went out to meet a friend on 17 September.
Selamaj was arrested at 3am on Sunday in Eastbourne, East Sussex, where he lived.
He has been remanded in custody to appear in Willesden Magistrates court on Tuesday.
A statement from the Crown Prosecution Service said: “The Crown Prosecution Service has authorised the Metropolitan Police Service to charge Koci Selamaj, 36, with one count of murder. The charge relates to the murder of 28-year-old primary school teacher Sabina Nessa in Kidbrooke, south-east London, on Friday, 17 September 2021.
“The CPS London Homicide Unit authorised the charge following a review of a file of evidence received from the Metropolitan Police Service.
“The defendant’s first court appearance will take place on 28 September 2021.”
Two men were separately arrested on suspicion of murder but were subsequently released under investigation.
A post mortem at Greenwich mortuary was inconclusive.
Ms Nessa was a teacher at Rushey Green primary school in Catford.
On Friday evening, hundreds of mourners including tearful relatives gathered for a candlelit vigil in memory of the teacher.
Ms Nessa’s sister Jebina Yasmin Islam broke down in tears as she addressed crowds.
She said: “We have lost an amazing, caring, beautiful sister, who left this world far too early.”
Ms Nessa, a graduate, studied at Greenwich and Bedfordshire universities.
Headteacher at Rushey Green Primary school Lisa Williams described her as a “brilliant and caring” teacher.
Specialist officers have been supporting Ms Nessa’s family at their Bedfordshire home.