Thomas Lomas, boss of Kent company Channel Livestock, admitted transporting the animals in a way likely to cause undue suffering.
Two sheep drowned and more than 40 were destroyed during an incident at the port on 12 September 2012.
Lomas was given a six-month sentence suspended for two years.
He was also ordered to pay £5,000 costs by Dover magistrates.
The sheep had to be put down after the lorry carrying them was stopped at Ramsgate by animal health inspectors.
Vets who examined the animals found that one had a broken leg, another was sick and more than 40 were severely lame.
The RSPCA said at the time none of the animals could reach their drink holders in the vehicle.
In a separate accident, a loading area floor collapsed while the sheep were taken off the lorry, which was carrying 548 animals.
Six fell in the water, with four being rescued by RSPCA officers, but two animals drowned.
Lomas's company was also fined £4,000 and ordered to pay £10,000 in costs.
After the hearing, Mark Rolfe of Kent Trading Standards said: "The law requires that those who engage in the transport of live animals take every step possible to prevent their injury.
"We believed in this case that wasn't the situation, the court have agreed with us and we are very satisfied with that result."
Laura Sandys, Conservative MP for South Thanet, said: "I hope it will send a message to anybody else thinking about operating this trade.
"It is a message to drivers that they do need to have proper training and expertise."
The case against two French drivers also charged after the incident was adjourned.