The 23-year-old, capped once by South Africa, joined Boro after leaving Peterborough United last summer.
Ntlhe made 24 appearances for Darren Sarll's side as they just missed out on the fourth-tier play-offs last term.
The announcement of his departure comes after Stevenage confirmed the signing of former Millwall left-back Joe Martin on Tuesday.
Stevenage left-back Kgosi Ntlhe has been released after just one season with the League Two club.