The man, aged in his 30s, who was wearing a tracksuit, a cap and fingerless gloves, scaled the bridge about 4.30am on Wednesday.
Just after 9.30am, the man surrendered to authorities and climbed toward Police Rescue officers who handcuffed him.
"We can confirm the man is in police custody and is safe," NSW Police tweeted. He was placed on a stretcher and taken to an ambulance by paramedics.
"The man is in a stable condition and will be taken by road to St Vincent's Hospital for further assessment," said a NSW Ambulance in a statement.
During the incident, two Special Operations Team paramedics had also ascended the bridge in harnesses to assist police in the event that the patient required sedation.
Traffic across the city was thrown into chaos during the incident, with authorities having to close several northbound lanes on the bridge as negotiators talked with the man.
By 8am, traffic heading to the bridge was backed up more than 20 kilometres in both directions.
All bridge lanes reopened at 10am, but motorists were warned by the Transport Management Centre that significant delays would continue during the morning.
Buses across the bridge are delayed by up to 70 minutes, but trains are running as normal.
Climbing the Sydney Harbour Bridge is illegal unless authorised and trespassers can be fined $3000.
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