It was rolled out in part of the city in 2014 while the African National Congress (ANC) was still in power, to encourage people to cycle.
Opposition parties had criticised the ANC, saying the money should be used to provide services for poor people.
Mayor Herman Mashaba, says the project would only be looked at, once all the city’s roads had been tarred.
He is from the Democratic Alliance which won control of the city in August elections, with the support of the Economic Freedom Fighters (EFF).
The EFF had marched to former mayor Parks Tau’s office, unhappy that the city had set aside 70 million rand ($490,000; £370,000) for cycle lanes in rich areas of the city while residents in Alexandra township still lived in squalid conditions.
The news of the cycle lanes received a mixed reaction when it was announced in 2014.
While some felt it was a vanity project for the city’s growing elite, others welcomed the vision of encouraging more residents to get out of their cars and cycle instead.
However, the move to halt the project has largely been welcomed.
The decision seems to show the influence of firebrand Julius Malema, whose EFF was merciless in its criticism of the lanes during its election campaign.
The EFF joined forces with the DA, which now runs Johannesburg.
The debate about infrastructure v the needs of the poor is a longstanding one here and it is a difficult balancing act.
Johannesburg fancies itself a world class city and meeting that ambition comes with a hefty price. But its managers also have to wrestle with the reality that many residents are still without basic services such as housing, water or proper sanitation, or proper roads. -BBC