Anti-drug enforcement and custom officials found the narcotic hidden in a container that was booked for Malaysia.
"We found the substance hidden in a refrigerated container at the Karachi port trust" a senior customs official said.
He said the culprits had hidden the drug in nearly 5400 bags concealed by solution tapes and balloons.
"We used sniffer dogs to find the drug as all the bags were de-stuffed and thoroughly examined. We found 830 pouches each weighing between 145 grammes to 155 grammes. The total weight of heroin was 125 kilogrammes," an official named Babar Ali Shah told media persons in the city.
"We have arrested the clearing agent and one of his employees," Shah said.
Shah said the seizure was the second biggest haul in Pakistan's history.
He said the value of the heroin in the local market was around USD 0.55 million but USD 13.75 million on the international market.
He said the narcotic hidden in a container was booked for Malaysia.
Anti drug-enforcement and custom officials say the drug is mainly smuggled into Pakistan from neighbouring Afghanistan through the northwestern province of Khyber Pakhtunkhwa, then sent by sea into the international market and sold at much higher value.
Last year in May the authorities seized 375 kilogrammes of the drug.
Officials say since the Soviets invaded Afghanistan and following the 9/11 incident, the close proximity to the neighbouring country and its vast mainly unmanned border, tribal areas were a hot spot for drug smugglers.
"They focus on smuggling in the drug from Afghanistan through the tribal areas and than try to smuggle it into international market for huge profits," Shah said.
Pakistan has more than four million drug addicts in a population of nearly 180 million, according to figures compiled by the Anti Narcotics Force, which is responsible for investigating and prosecuting drug offences in the country.
Pakistan has a 2,500-kilometre porous border with Afghanistan, which supplies 90 per cent of the world's opium used to make heroin.