The case will now be heard afresh at a lower court with the High Court directing that the two be taken to police custody for the preparation of plea taking before July 7, reports Xinhua news agency.
Wanyama and Obara were convicted last year for an incident in 2018 where they were accused of jointly raping an upcoming musician.
In quashing their sentence, the High Court ruled existing records do not show whether one of the witnesses who testified for the prosecution was sworn in or not.
Original trial Magistrate, Martha Mutuku, said the victim was traumatised by the event which took place at a Nairobi apartment on February 11, 2018.
The victim claimed that on the fateful day, which was her birthday, she attended a party in Kilimani residential state in upmarket Nairobi where the two rugby players were present.
In her statement to police, the victim said that she only knew one of the two rugby players and after a night of fun she accompanied the pair to one of their homes.
At the apartment, the victim narrated how she was raped in turns despite her pleas to stop while the defendants argued what transpired was consensual.
The prosecution further argued consent obtained under the influence of alcohol is not admissible in a case that shocked the entire rugby fraternity in Kenya.
In the aftermath, the Kenya Rugby Union held a series of workshops and seminars to encourage players to observe caution, especially when dealing with fans.