Mr Scott, who denied mistreating the animals, collected dozens of signatures from his customers on a petition in a bid to clear his name.
However, Ray Scott, 54, of Ringstead Garth, Bransholme, was found guilty of failing to give the animals a nutritious diet and seek treatment for those that were sick.
The offences took place around June 1 last year at the pet shop, a sentencing hearing at Hull Magistrates’ Court heard earlier this week.
RSPCA inspector Sarah Keith said: “These animals were not being looked after in the way they should have been.
“Despite our best efforts to work with Mr Scott, he continually ignored our advice, leaving no other option but to go down this route.”
The court heard RSPCA inspectors first visited the pet shop after a call from a concerned member of the public on April 14 last year.
On June 1, 33 rabbits and 19 guinea pigs were seized by police on vet advice after improvements were not made.
Inspector Keith said: “Rabbits and guinea pigs need the things all animals need – an appropriate diet and an appropriate environment to live in as well as vet care if they are sick.
“These animals did not receive these most basic of things in the care of Mr Scott.
“If he can’t provide these things he shouldn’t be allowed to keep animals and I am pleased he has been banned from doing so.”
After the hearing, Mr Scott said he was disappointed, but not surprised, by the outcome.
He said: “We could not afford to pay for an expert to fight our corner. More than 100 people signed my petition, stating I looked after the animals well.”
Mr Scott said the shop would remain open but only sell pet supplies.