Shaharyar, 80, also held the post from 2003-06 before being removed by the government following the infamous ball-tampering controversy which led to the team forfeiting a test match against England.
Pakistan refused to play on in protest after Australian umpire Darrell Hair penalised them during the fourth test at The Oval.
An inquiry by the International Cricket Council eventually cleared the players of ball-tampering.
"It is notified that Shaharyar M Khan, i.e. the sole candidate for the office, has been unanimously elected as chairman of the PCB," the Pakistan Cricket Board said in a statement.
Shaharyar's return for a three-year term came in a new electoral process held under a fresh board constitution.
It ended a period of turmoil during which his predecessors, Najam Sethi and Zaka Ashraf, were involved in a bitter tussle for the job.
Shaharyar's election came three months after the Islamabad High Court declared Ashraf's election null and void.
The court twice reinstated Ashraf, bringing about chaos and uncertainty because the government had also appointed Najam Sethi as chairman in June.
Several former players described the 'musical chairs' confusion as a comedy of errors and bad for the image of Pakistan cricket.
Last month the Supreme Court accepted a new constitution and appointed a caretaker chairman and election commissioner. The repeated reinstatements by the Islamabad High Court were also declared null and void.
"Let us hope there is now some semblance of order and continuity in Pakistan cricket affairs," said former chief executive Arif Abbasi.
Shaharyar immediately gave his support to captain and senior batsman Misbah-ul-Haq who is under-fire following Pakistan's 2-0 test series defeat by Sri Lanka earlier on Monday.
The career diplomat told reporters that Misbah, 40, would remain in charge until the 50-over World Cup in Australia and New Zealand next year.
"I am not going to press any panic button," he said. "I believe in continuity in cricket matters and a few bad results don't mean we start talking about removing Misbah as captain."
Misbah has been test captain since 2010 and ODI skipper since 2011. (Editing by Tim Collings)