The man, aged in his 40s, 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 and brought him down.
"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.
Traffic across the city was thrown into chaos during the incident, with authorities having to close several lanes as negotiators talked with the man.
By 8am, traffic heading to the bridge was backed up more than 15 kilometres in both directions.
Buses across the bridge are delayed by up to 30 minutes, but trains are running as normal.
Climbing the Sydney Harbour Bridge is illegal unless authorised and trespassers can be fined $3000.
