Bafana need a point to book their ticket to Egypt, while Libya need maximum points to qualify for Afcon.
The nations square off on March 23 in Egypt. They shared the spoils in the first leg at Moses Mabhida Stadium in Durban.
Khune has been ruled out for six months after sustaining a shoulder injury.
Bafana coach Stuart Baxter has been consistent with his selection in the goalkeeping department but an injury to Khune will force him to call a replacement for the country's incumbent shot-stopper.
Ronwen Williams is likely to earn another call-up and is set to deputise for Keet between the sticks.
The big question is who will be the third goalkeeper.
The battle is among Siyabonga Mpontshane of Orlando Pirates, AmaZulu’s Siyabonga Mbatha and Nkosingiphile Gumede of Lamontville Golden Arrows.
Baxter doesn’t have a lot of options. Most teams in the Premier Soccer League boast foreigners in their goalkeeping departments.
Defending league champions Mamelodi Sundowns have Denis Onyango from Uganda and Kennedy Mweene from Zambia, while Cape Town City possess Peter Leeuwenburg (from Holland).
Polokwane City have Zimbabwean George Chigova in their last line of defence and Maritzburg United rely on Richard Ofori from Ghana.
Tapuwa Kapini commands the number one position for Highlands Park and Free State Stars have shown faith in Badra Ali Sangare of Ivory Coast, while Baroka FC have found their new hero in Elvis Chipezeze from Zimbabwe.
So Baxter will have to look at Mpontshane, Gumede and Mbatha to complete his goalkeeping department, which is likely to be led by Keet.
Keet has been consistent this season for Wits. He has conceded the least number of goals after 17 matches. Keet has let in 12 goals and has kept eight clean sheets and will head into Bafana camp brimming with confidence.
Keet is also experienced, having played in the Afcon and in continental competitions for the Clever Boys.
Bafana have conceded one goal in the Afcon qualifiers. They have kept four clean sheets in five matches and will need one of those if they are serious about going to Egypt.
Bafana are second with nine points after five games, one point behind the Super Eagles of Nigeria, who have already secured their place in Egypt.
Bafana missed out on the last Afcon in Gabon and will be looking to make it this time around in Egypt, especially after failing to book a place in the World Cup in Russia last year.@minenhlecr7