Speaking about Mr Mahathir's behaviour during his first prime ministership, Ibrahim Suffian, executive director of the Merdeka Center, an independent survey group, said: "Many of his allies suffered during his time as prime minister".
Malaysia's new Prime Minister Mahathir Mohamad sought a pardon for Mr Anwar, which was granted on Wednesday morning.
Jack Seng, another supporter wearing a shirt with a logo of Anwar behind bars, said he thought Mahathir and Anwar would resolve any tensions between them.
An advocate for reform, clean government and an end to the previous government's authoritarian ways, Mr Anwar made no immediate comment but was expected to address the public in the afternoon followed by a political rally in the evening. Both times, he and his supporters have said the charges were politically motivated.
He has been in hospital for a few months recovering from a shoulder operation.
Mahathir has named just three ministers so far in addition to himself and Anwar's wife, Wan Azizah Wan Ismail, as deputy prime minister.
It is a step that can be immediately pursued, rather than waiting the five years stipulated in the country's constitution, due to a royal pardon from Malaysia's king.
On another question if the Election Commission chief Tan Sri Mohd Hashim Abdullah will be changed, Dr Mahathir said: "If he has done anything wrong, the normal process will apply to punish people who had done the wrong things".
Anwar was found guilty and sentenced to jail in 1999, but was released in 2004 after his sodomy verdict was overturned.
The corruption-plagued former government of now-disgraced Najib Razak was keenly aware of this, and the latest sodomy charge dogged Anwar through a lengthy trial that culminated in his imprisonment in 2015.More news: Juventus clinches seventh consecutive Serie A title
In an astonishing U-turn past year, Anwar shook hands with Mahathir and agreed to join forces to oust scandal-tainted Najib.
"My answer is simply that we must all firmly resolve to never let our nation sink to the depths it did again and prime minister Mohamad now has a rare second chance to put things right". "There will be no special powers given except as are given to ministers or deputy ministers or deputy prime ministers", Mahathir said.
"I don't need to serve in the Cabinet for now", he said.
Previously, the charismatic Anwar headed various ministries under Mahathir's tutelage in the 1990s, earning praise as a reformer.
Differences have already cropped up between supporters of Mahathir and Anwar over cabinet positions and Anwar's role.
He must first be elected to parliament, having been stripped of his seat in 2015 when his conviction on charges of sodomising a young male aide was upheld on appeal, sending him to jail.
Separately, Malaysia and six countries are investigating defeated prime minster Najim over corruption at the state fund 1MDB.
He said: "They couldn't get here without Mahathir, and they're not about to abandon him".
"It looks very likely that Najib will face the full force of the law", said Adib Zalkapli, a Kuala Lumpur-based analyst with risk consultancy Vriens & Partners.