At dawn, three protestors lowered themselves from a public walkway where they unfurled red flags and banners with the slogans, "100% renewables" and "make coal history".
Security staff raised the alarm around 5:15 a.m (1915 GMT Monday) after protesters climbed the landmark bridge.
They were all conditionally bailed, charged with climbing the bridge and willfully preventing the free passage of a person/vessel.
Police arrested 10 people earlier this morning before arresting the final three, who were attached to ropes beneath the bridge, about 9.30am, bringing the operation to a close.
Ten were taken to local police stations for questioning.
Thirteen people have been arrested after environmental group Greenpeace called on Prime Minister Scott Morrison to "declare a climate emergency" by protesting on the Sydney Harbour Bridge on Tuesday morning.
The protest was co-ordinated by Greenpeace Australia Pacific, which said the protesters were "specialist trained climbers" who were calling "attention to the climate emergency".
Some were detained by security officers who called the police but three avoided detention and carried on with the planned protest.
"Coal is the number one driver of climate change in Australia - we urgently need a plan to phase out coal power to be replaced by clean energy", he said.
"Right now people are wanting action on climate change, they want a government that takes the issue seriously and takes real action", she told Sky News on Tuesday.
The Government have also had their input on this morning's protest, with Prime Minister Scott Morrison saying that taking action on climate was "important", but said protesters needed to be considerate of others.