Anwar was heir-apparent to the premiership until Mahathir sacked him in 1998 and he was subsequently jailed for sodomy and abuse of power.
That conviction is viewed by many as having been orchestrated by Najib's government to neutralise Anwar's rising political threat. Anwar is expected to be released this week, as early as today.
From there, Anwar left for his home in Segambut, Kuala Lumpur where he expressed his gratitude to the King for pardoning him and to the prime minister for assisting with the process of his release.
"Freeing Anwar was a long time coming, and, while people in Malaysia and around the world are delighted, no one should forget the injustice he faced serving a long sentence for a crime that should never have been considered a crime", he said.
His daughter, lawmaker Nurul Izzah Anwar, said the Pardons Board will meet on Wednesday, after which Anwar is expected to be released.
Anwar had been recovering from a shoulder injury in hospital under police guard.
A four-party alliance driven by Mahathir and Anwar won the general election last week, ousting the ruling Barisan Nasional coalition for the first time in the history of the Southeast Asian nation.
"I hope I will be given some space to spend time with my family although at the same time, I need to give support to my wife (Datuk Seri Dr Wan Azizah Wan Ismail), who is now the Deputy Prime Minister".
Anwar said that after working with Mahathir for many years he understands "that he cares deeply about Malaysia and the people of Malaysia".
Dr Mahathir said the focus on corruption was important especially 1MDB as well as money that had been misappropriated by the previous government.
Differences have already cropped up between supporters of Mahathir and Anwar over cabinet positions and Anwar's role.
Mahathir said it would be hard to achieve consensus and any decisions will be based on the voice of the majority.
But the two men fell out over a number of issues, resulting in the popular Anwar's imprisonment, which triggered unprecedented protests.
The Malaysian Islamic Party (PAS) emerged as the third biggest force with 18 seats.
Anwar's trial became a spectacle, with prosecutors at one stage bringing out what they said was a semen-stained mattress allegedly used when he had sex with two male aides.
He was then convicted and jailed again for a second five year on a second trumped up sodomy charge during the rule of Najib. He led an opposition alliance to major gains in the last two elections, winning the popular vote in 2013. "Authoritarian leaders always believe the best way to deal with dissidents is to jail them, but throughout history, it has always backfired".
But voters resoundingly rejected the government of scandal-tainted Najib Razak and voted in an opposition alliance, triggering a series of dizzying developments - with Anwar's release perhaps the most dramatic yet. Mr Apandi cleared Mr Najib of any wrongdoing in connection with the misappropriation of billions of dollars from 1MDB.
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