The trio committed the attack on the World Heritage Site just a day before last year's Summer Solstice.
Rajan Naidu, 74, Niamh Lynch, 23, a student from Oxford, and Luke Watson, 36, committed the attack just a day before last year's Summer Solstice.
Mr Naidu and Ms Lynch were accused of using two colour blasters with cornflour, talc and an orange dye inside to spray the iconic site.
Mr Watson had bought the equipment and drove his accomplices to Stonehenge that morning.
They admitted taking part in the protest and said in their defence they had a "reasonable excuse" – their right to freedom of speech and freedom to protest under Articles 10 and 11 of the European Convention on Human Rights.
The three culprits denied charges of damaging an ancient protected monument and causing a public nuisance.
The trio were acquitted on Friday after a 10-day trial at Salisbury Crown Court.
After the attack, Naidu and Lynch, who were both wearing white Just Stop Oil T-shirts, sat down in silence in front of the stones until they were arrested by the police.
The court heard the stones were promptly cleaned and the costs of removing the powder totalled £620.
Simon Jones, prosecuting, said: “Putting it simply, we say they were all in it together.
“The prosecution say that this is an act of blatant and clear vandalism. The intention is undoubtedly to make a statement.”
Mr Jones added: “Stonehenge is arguably the best recognised and architecturally sophisticated prehistoric stone circle in the world, built around 5,000 years ago.
“The site in Wiltshire is visited by members of the public from all over the world, providing both an education and spiritual experience.“The stones are a protected ancient monument.”
Speaking after the jury found the three Just Stop Oil activists not guilty, Naidu, said: “The judicial system must wake up and begin to play its shamefully neglected role in defending us and other species from rapacious billionaire class climate criminals.
“We need a global Fossil Fuel Non-proliferation Treaty right now.”
Lynch, who is now a masters student in ecology and conservation at the University of Exeter, said: “I just want things to be better, I just want things to be fair and right.
“If you see something you love being hurt, you do everything you can to help. It’s quite simple. It’s totally natural.“I might not be able to do much but I categorically refuse to do nothing. I refuse to stand by and watch as our world burns around us.”
Watson, a carpenter, added: “I’m glad of the verdict but feel the last two weeks have been a complete waste of public money and that a case involving £620 of damage should have been dealt with in the magistrates court.”
It comes just days after two Just Stop Oil activists who sought to spray orange paint on Taylor Swift's private jet were spared jail.
Jennifer Kowalski, 29, and Cole Macdonald, 23, had been targeting the pop star's jet at Stansted Airport in Essex but the two planes they sprayed on June 20 last year belonged to an insurance firm and an investment group.
