The freed Indians were now on their way to the border city of Lahore from where they would head home to India.
The Superintendent of jail in Malir, Ghulam Qadir, said that the 89 fishermen were released and sent by two buses to the city of Lahore from where they will be handed over to Indian authorities at the Wagah border crossing.
The fishermen were released just two weeks after the Prime Ministers of India and Pakistan met in Mohali on the sidelines of the World Cup semi-final match between the two countries.
Their release was a follow-up to a meeting of the Interior and Home Secretaries of India and Pakistan in New Delhi last month. Both countries had exchanged lists of prisoners during the meeting of the Interior and Home Secretaries.
"The prisoners were released today and given some personal belongings, gifts and money to help them in their journey," Qadir said.
He said the fishermen were arrested from Pakistan`s waters in violation of the maritime agreement between both countries over the last two years.
Qadir said hopefully the Indian fishermen would cross the Wagah border tomorrow.
Nasir Aslam Zahid, Chairman of the NGO Prisoners Welfare and Legal Aid Committee, told reporters that Pakistani authorities had granted consular access to another 33 Indian prisoners being held in Malir Jail.
They too will be released in the near future after the completion of certain formalities, he said.
"It is our endeavour to remove hurdles and delays in the release of detained fishermen on both sides of the border," Zahid said.
On April 11, India released 39 Pakistani prisoners.
The two countries are scheduled to exchange complete lists of prisoners on July 1 under an agreement on consular access signed in May 2008.
The process of releasing prisoners, which suffered a setback in the wake of the Mumbai attacks in November 2008, has picked up pace after the two countries recently agreed to resume their stalled peace process.
Pakistan and India frequently seize each other`s fishermen, accusing them of violating their respective zones in the Arabian Sea.
Last year in September Pakistan released around 100 prisoners, including 80 fishermen jailed in Karachi.
The Indian prisoners released today were arrested between September 2009 and January last year, TV news channels reported.