The malnourished mother and her youngster were found traumatised and hugging one another when they were saved by International Animal Rescue.
Frightened locals reportedly hurled rocks at them and tried to tie them up.
Rescuers say the mother, who was extremely thin, had sustained wounds to the skin.
Primates escaping forest fires in Indonesia often head to villages in search of food, but many locals view them as pests - resulting in an increase in human-animal conflict.
The International Animal Rescue (IAR) team said that the two primates were rescued just in time. They say that the mother had just enough milk to nourish the baby.
She was also injured by a rope that had been tied around her wrist.
The rescue team anesthetised both animals in West Kalimantan province last month so that they could be safely released after medical tests to a protected area of forest for monitoring.
Many apes have been forced to flee their forest homes to escape thousands of forest fires that have engulfed the country this year.
Many of the fires were illegally started for land clearance purposes and have raged out of control in the dry weather conditions.
The UK-based IAR says that it has carried out more than 12 operations over the last two months to save orangutans that have strayed from their natural habitats.
Many Indonesian forests have for months been shrouded in thick haze caused by the fires, which in turn has contaminated air across neighbouring countries in south-east Asia.

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The Ross County striker transferred his prolific club form onto the international stage to beat the All Whites in the friendly in Belfast.
"My family were all in the stands so to score in front of all of the fans and hear the noise of a goal was unreal.
"I thought I took my goal well, it's a brilliant feeling," Boyce said.
Boyce was unlucky to be omitted from Michael O'Neill's squad for the Euro 2016 finals but finished this season as the Scottish Premier League's top-scorer with 23 goals, including 10 in his last 10 games.
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With forwards Conor Washington and Jamie Ward out injured, Boyce seized his chance and said the early goal after just six minutes was exactly what he wanted.
"The form I've been in you want to get a goal as early as possible and try to add to that," said Boyce.
"I cut inside and hit it well between the defender's legs and once that happens, more than likely it's going to go in."
Boyce is determined to make an impact in Northern Ireland's World Cup qualifier away to Azerbaijan on 10 June by scoring his first competitive goal.
"It's not so long ago I was playing in the Irish League and I want to show I'm better than that and see how far I can go in football," added the ex-Cliftonville man.
Northern Ireland manager Michael O'Neill described Boyce's display as evidence of "a player on top of his game".
He admitted he was "slightly disappointed" the team did not add further to their tally.
"It was a physical game, a demanding game, which was exactly what we wanted.
"It leaves us in a good place for next week."
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A rare Borneo orangutan and her baby have been rescued from an attack by angry villagers in Indonesia as they were escaping rampant wildfires.
[NEXT_CONCEPT]
Liam Boyce described the feeling of scoring his first international goal as "unreal" after netting the winner for Northern Ireland against New Zealand.