The Reverend Sue Parfitt, Father Martin Newell and former university lecturer Philip Kingston targeted a service at Shadwell, east London, halting 14 others.
Mr Kingston, 85, glued his hand to a carriage while Rev Parfitt, 79, and Fr Newell, 54, climbed on to the roof and said prayers for the planet before they were dragged off by commuters.
Jurors at the Inner London Crown Court ruled they were exercising their right to peaceful demonstration in October 2019.
The verdict comes soon after four people were cleared of criminal damage after toppling a statue of slave trader Edward Colston
Tory MP Tom Hunt said: “I suspected that the disappointing Colston statue verdict might be a green light for other criminal acts.
“Those committing vandalism and damaging public property, or blocking public access like roads or railways, should be punished.
“I am disappointed to see another instance where this has not been the case.”
His fellow Tory MP Brendan Clarke-Smith added: “The selfish actions and egos of these individuals prevented people from getting to work. This outrageous decision has given the green light to people looking to commit all manner of appalling crimes in the name of religion to justify their extreme political ideologies.”
Six members of the Extinction Rebellion group were found not guilty of the same offence at Canary Wharf in April 2019.
Extinction Rebellion protesters were also cleared of causing criminal damage to Shell’s London headquarters in April last year.
Rev Parfitt said the verdict showed the protest had been “the right thing to do. It’s wonderful that the jury saw the bigger picture, that the court has vindicated our action and we hope it in some small way inspires others.”
The trio said they were motivated by their Christian faith, while Mr Kingston said the futures of his four grandchildren also prompted him to protest to the public and the Government about the dangers of climate change and the financial institutions involved. Meanwhile, an Insulate Britain campaigner who went on a 26-day hunger strike in prison said her time inside had “made her focus” on her campaigning.
Emma Smart was freed from HMP Bronzefield in Surrey yesterday alongside retired GP Dr Diana Warner – they were among six activists jailed for breaching an injunction against road protests.
Supporters cheered as Ms Smart punched the air. Four other Insu-late Britain members left Thame-side jail in south-east London.