The video has been viewed nearly 200,000 times and shared nearly 6000 times.
Ms O'Brien told news.com.au the puppies were clearly suffering in the heat and leaving them behind was distressing.
"It definitely shattered my heart," she said.
"I was with my mum at the time and when we were walking off we turned around to see two of the pups standing against the side of the cage watching us.
In a statement, Parklea Markets said temperatures inside the markets were significantly lower than outside on hot days.
"Parklea Markets takes the issue of animal welfare seriously," the statement said.
"The pet stalls at the markets are regularly inspected by and comply with the guidelines set by agencies such as RSPCA.
"The stallholders monitored the temperatures within the markets throughout yesterday.
"Misting fans were also in use.
"Once the temperature reached the upper limit, removal cages were brought in and the animals were removed."
The market spokesman said all pets were removed on Saturday as temperatures climbed even further.
Ms O'Brien said she believed all the animals at the market were suffering from heatstroke.
"There were around nine or 10 puppies, a few kittens in the back cages," she said.
"You can see one on the video with its mouth ajar and clearly panting, which isn't very common in cats, only in extremities.
"(It) goes to show how much they were suffering.
"There were a few rabbits and guinea pigs in one or two cages, and it's well known for rabbits to pass away in high temperatures."
"There were three cages stacked on top of one another, (the) top with turkeys, bottom with hens and the middle was extremely overcrowded with chicks and ducklings.
"It almost seems like they're standing on top of one another as they are crammed and squished together," she said.
"I've grown up with dogs and cats and the characteristics they possessed were definitely symptoms of heat stroke."
A RSPCA spokeswoman said an investigation was underway after the protection agency was inundated with complaints.
People signing the petition have reacted with outrage.
Ms O'Brien said the animals had been moved when she returned to the markets this morning.
"I have gone back today, as well as a number of people, and the dogs, cats, rabbits and guinea pigs have been moved [with a sign saying it was] because it's 'too hot'," she said.
"However, they were there yesterday."
She said she believes the market only moved the animals due to the online backlash.
The pictures came after the NSW RSPCA said on Friday that multiple dogs had died across the state this year due to repeated extreme heatwaves.
The Queensland RSPCA is also investigating after a dog died of heatstroke after being tied up without shade or water in a Hervey Bay backyard.
A neighbour told the animal welfare organisation after noticing the dog had died in the backyard at Urangan on Saturday morning while tethered on a rope.
The Parklea Markets spokesman said an internal review would be undertaken to determine if animal welfare procedures where adhered to on Friday.
