Buildings were evacuated earlier and people warned to avoid parts of the city due to an "industrial incident", West Yorkshire Police said.
The force said the crane had "been made safe without incident" and the cordon was no longer in place.
Evacuated residents have returned to their homes and roads closures have been lifted.
At the height of the disruption, train services were affected at nearby Leeds Railway Station but have since resumed.
Earlier, onlookers were reportedly told by police at the scene there was a danger a white tower crane operating close to Whitehall Road could collapse.
One onlooker, Luke Peters, 38, from Chapel Allerton, said the crane had looked "off-kilter" and confirmed the police had told him it could fall over "imminently".
He added: "I wouldn't want to be going for a run along the river right now."
Access to the Riverside Way area was restricted for pedestrians and road closures put in place.
A cordon was also put on a stretch of Whitehall Road, a short distance from Leeds Station, and riverside paths were also closed and guarded by officers.
A nearby Premier Inn hotel was among the buildings evacuated.
West Yorkshire Fire & Rescue Service said it was called to reports of an unstable structure on Riverside Way at about 13.35pm.
It said the crane had been made safe at about 17:30 BST and all crews had now left the scene.
The crane was one of two around a half-built tower block between the road and the River Aire.
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A cordon put in place due to concerns about an "unstable" crane in Leeds city centre has been removed.