Sri Lanka have never won a home one-day series against Pakistan before and are now eyeing a clean sweep.
Mahela Jayawardene scored a brisk 123 for his first one-day century in two years to help Sri Lanka overhaul a daunting 289-run target at the Rangiri International Stadium.
Pakistani former captain Zaheer Abbas said the defeat stressed the need for a major overhaul.
"The World Twenty20 win had hid all the weaknesses in the team and the cricket board," said Abbas, referring to Pakistan's triumph in England in June.
"The top man doesn't know much about the intricacies of cricket and is taking decisions to please his friends," Abbas said of Pakistan Cricket Board (PCB) chairman Ijaz Butt. "From top to bottom we need changes.
"Since this board has taken over we have lost the Champions Trophy, we have been stripped of World Cup 2011 matches and we have failed to handle the team, so this is total mismanagement, which is unacceptable," said Abbas.
Security fears in Pakistan forced the International Cricket Council (ICC) to relocate the biennial Champions Trophy to South Africa in February. Two months later, the ICC also had to move World Cup 2011 matches out of Pakistan.
"The coach (Intikhab Alam) must go, and the captain (Younus Khan) also lacks the qualities of a good leader," said Abbas.
Former chief selector Abdul Qadir demanded resignations from the board and the team.
"They should feel ashamed," said Qadir, who resigned in June after alleging interference in selection matters from the PCB and Alam.
"Defeats are part and parcel of the game, but shameful defeats are unacceptable."
Former captain Aamir Sohail, who last month resigned as the PCB's development director after differences with management, also slammed the Pakistani setup.
"No one, from the board officials to the team management, seems to have a clear plan in mind," he said.
"Some of the decisions make no sense, like two regular openers were sent to Sri Lanka but we used makeshift openers in the series which we have lost now."