The decision comes after a court found TT-Line, which has operated the service for 37 years, guilty of breaching animal welfare laws over the deaths of 16 polo ponies on a summer Bass Strait voyage.
The horses had competed in a tournament in Tasmania and were travelling from Devonport to Melbourne in a converted refrigeration trailer on the night of January 28, 2018.
They were discovered dead when the trailer was opened at Yarra Glen in regional Victoria at about 7.15am the next day. Two horses, named Scarlet and Delilah, survived.
TT-Line was on Thursday found guilty in Burnie Magistrates Court of breaching 29 animal welfare laws.
Magistrate Leanne Topfer ruled the company made no inquiries to ensure the horses were individually stalled, per regulations, or ensure adequate ventilation.
In a statement on Saturday, TT-Line announced it would no longer carry livestock "effective immediately and until further notice".
The company said it was acting on legal advice following the court decision.
"TT-Line is working to resolve the matter as quickly as possible," it said.
TT-Line is expected to return to court for sentencing on December 21.
The company has been operating ferries between mainland Australia and Tasmania since 1985.
The Tasmanian Labor opposition said the decision by TT-Line was a concern for the horse industry and would have a huge impact.
"This will impact the racing and breeding industry but also junior competitors in pony club, recreational and amateur riders looking to compete in national competitions, as well as any person needing to transport a horse to or from the mainland," party leader Rebecca White said.
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