Baartman was withdrawn from the South Africa line-up for an undisclosed medical reason unrelated to Covid-19 after all squad members returned negative tests twice before boarding the plane for Pakistan.
Left-arm seamer Jansen does not boast a lot of domestic experience with just 12 first-class appearances but he has forged a reputation for being a lethal customer with the ball. He has taken 21 wickets at an impressive average of 20.71 during this summer's four-day competition and has featured for South Africa A in the past.
The inclusion of Jansen allows the Proteas to keep their power-packed pace battery intact without any fears of reduced numbers.
South Africa's touring contingent has left for Pakistan and will arrive in Karachi later on Saturday. The tour comprising of two Tests and three T20Is marks the team's first trip to Pakistan since 2007.
The team will be led by Quinton de Kock with the likes of Kagiso Rabada and Dwaine Pretorius making a comeback to the side after missing the home series against Sri Lanka.
Revised South Africa squad: Quinton de Kock (capt & wk), Temba Bavuma, Aiden Markram, Faf du Plessis, Dean Elgar, Kagiso Rabada, Dwaine Pretorius, Keshav Maharaj, Lungi Ngidi, Rassie van der Dussen, Anrich Nortje, Wiaan Mulder, Lutho Sipamla, Beuran Hendricks, Kyle Verreynne, Sarel Erwee, Keegan Petersen, Tabraiz Shamsi, George Linde, Daryn Dupavillon, Marco Jansen