Extinction Rebellion Scotland members gathered at the premises in Altens at 6.30am on Thursday.
The group said about 30 activists stood at the three entrances, with some of the protesters locked together.
They blocked a road with XR Scotland's big purple boat, named Amal Gous.
Extinction Rebellion Scotland said they shut the building down to disrupt business and hold Shell to account for its role in the climate crisis.
Police said they were called to the scene at about 6.45am on Thursday, while the activists said there were no arrests and the protest finished at about 7.30pm.
An XR Scotland spokesman said: "Today's successful protest marked the final day of ten days of action focused on the fossil fuel industry, and in particular Shell's role in driving the climate crisis.
"Thirty activists spent 13 hours blockading the entrances to Shell HQ all day, sending a message that we won't take their wilful avoidance in the face of the climate emergency any more.
"In Aberdeen, the oil capital of Europe, we must put workers and communities first - not big business profits.
"However, in the face of wildfires across Australia and devastating flooding in Indonesia, Shell are stubbornly increasing their output of fossil fuels by 35 per cent. They do not value our futures.
"Today's protest is just the beginning, we will continue to take action until governments and industry respond sensibly and appropriately to the dire warnings of 11,000 scientists, David Attenborough and Mark Carney, the outgoing head of the Bank of England.
"Anything other than a rapid winding down of the fossil fuel industry is irresponsible and reckless."
One of the protesters, who gave his name as Paul, 43, from Aberdeenshire, said: ?"If the whole world reaches zero carbon emissions by 2030, we only have a 75 per cent chance of staying below (an increase of) 2C.
"These are terrible odds and by committing to continued production decades into the future, Shell is literally destroying our future.
"The more successful fossil fuel companies like Shell are, the worse our future is going to be. We have to stop them carrying on as if their product does no harm. "
The purple boat bears the words The Future You Fear Is Already Here, a reminder that "catastrophic" climate change is already under way across the planet.
The action is part of Rig Rebellion 2.0, a two-week campaign by Extinction Rebellion Scotland targeting the fossil fuel industry and the institutions which support it.
A Shell spokesman said: "The heightened awareness of climate change that we have seen over recent months is a good thing.
"As a company, we agree that urgent action is needed.
"What will really accelerate change is effective policy, investment in technology innovation and deployment, and changing customer behaviour.
"As we move to a lower-carbon future, we are committed to playing our part, by addressing our own emissions and helping customers to reduce theirs - because we all have a role to play."
Police said officers were at the scene of a "peaceful protest" outside the Shell premises.
Chief Inspector Davie Howieson, local area commander for Aberdeen South, said: "The road was blocked from around 6.45am on Thursday January 16 and road users are advised to avoid the area for the time being.
"We are liaising with both Shell and the protest organisers, Extinction Rebellion."