Mitchell was riding the seven-year-old bike when police officers refused to let him leave Downing Street via the main gate in September last year. It was claimed at the time that Mitchell swore at the officers and called them "plebs".
Mitchell - who strenuously denies the allegation that he called the officers "plebs" - was forced to resign after a series of damaging headlines.
He put the 18-speed Reflex Westminster on sale to give it a "good home out of the limelight", and after a five-day auction the bike fetched £10,600 on eBay last night, which will go to Nyumbani UK, which helps HIV and Aids-affected children in Kenya.
The charity said the auction attracted more than 31,600 views over five days, with 60 bids in total, but the identity of the bike's new owner has not been revealed.
Mitchell said: "I am pleased it has raised so much for Nyumbani UK, which helps thousands of Kenyan children orphaned through the HIV pandemic.
"The auction has gone better than I thought it would and I hope the bike's new owner will enjoy riding it as much as I have."
Nyumbani UK chairman Simon Philips said the charity was extremely grateful, adding: "All proceeds will go towards providing these children with the best nutritional, medical, educational and psychosocial care and will definitely make a tangible difference to their lives."
Scotland Yard are investigating the Downing Street dispute in the wake of a Channel 4 investigation which cast doubt on the original account of the incident.
The programme revealed CCTV footage which showed there was not a large group of tourists outside the main gate at the time, as had originally been claimed.
An email from a civilian witness backing up the police account of events has also since been called into question.