The six-month-old dog, named Chula, was killed in 2008 when its owner kicked it after waking to find the animal had gone to the toilet inside his house.
The man admitted in court on Wednesday that he had kicked Chula, who was later taken to a local vet by the owner's girlfriend.
Despite receiving medical attention, the dog died of the serious internal injuries.
Two vets involved in the case went on to report the incident and animal protection agency El Refugio took Chula's owner to court.
Chula's owner has now been handed a three-month custodial sentence.
He has also been banned from carrying out "any trade or profession related to the care, custody or trade of domestic animals for the period of two years", according to Spanish daily 20minutos.
The law under which the man was prosecuted has changed since the time of the killing.
"If he had been judged under the current law the sentence would have been even longer," said Nacho Paunero of El Refugio.
"It is a giant step for the defence of animal rights in Spain," he added, before thanking the two vets who reported the incident for their involvement in "a bittersweet day".
The case is believed to be the first time a Spanish court has sentenced someone for animal cruelty.