Chief selector Mohsin Khan told a news conference on Wednesday that Younis had been included in place of Mohammad Yousuf [ Images ] who has been ruled out with a hamstring injury.
"Younis will join the national training camp from today and will be part of the one-day and test squads," Mohsin said.
Younis's comeback was made possible after he met Pakistan Cricket Board (PCB) chairman Ijaz Butt on Wednesday in Lahore [ Images ].
The talks broke the ice after Butt was not considered for selection for the Asia Cup and England [ Images ] tour and was initially left out of the squad for the South Africa series.
The PCB chairman had not given clearance for Younis to be considered for national selection since he last played in the ODI series in Australia [ Images ] in February.
Younis was among seven players either banned or fined by the board in March for indiscipline on the tour to Australia.
An appeals tribunal later lifted the bans, including that placed on Younis, but the PCB said he still needed to resolve some issues with the board because they were unhappy with some of the statements given by him and his lawyer in the media.
"The PCB chairman met with Younis today and gave clearance to the selectors to consider him for selection," Mohsin said.
"The return of Younis is a good sign for the team as he is a very experienced player and is now free to focus on his cricket."
Younis told reporters he was pleased his issues with the board had been sorted out.
"I am very happy and relieved to be back in the team and it will be my earnest effort to live up to the confidence imposed in me by the selectors," Younis added.
Younis, 32, has played 63 tests and 202 ODIs and last year led Pakistan to the T20 World Cup title in England.
Pakistan coach Intikhab Alam said Yousuf had suffered a grade A hamstring injury in their conditioning camp.
"Yousuf has been advised to rest for two to three weeks and that is why he is not available for the one-day and T20 matches against South Africa," Alam said.
Yousuf was named in the ODI and test squads last week before suffering the injury during the training camp in Lahore.