The 36-year-old Yousuf was practising at the ground when he felt groin problem and was replaced by young batsman Umar Akmal.
Pakistan also included two regular spinners, Saeed Ajmal and Abdul Rehman, at Dubai Stadium, which will be hosting a Test for the first time.
Team manager Intikhab Alam said Yousuf's injury was a recurring one.
"It's the old injury he picked up before the one-day series last month, so we thought it's not worth taking risk because it's a five-day Test," said Alam.
Pakistan has also given a Test cap to 25-year-old wicketkeeper Adnan Akmal, who replaces Zulqarnain Haider.
Haider fled to London on the morning of Monday's fifth one-day match against South Africa, saying he had received death threats.
South Africa's line-up includes both their spinners, Paul Harris and Johan Botha, with Dale Steyn, Morne Morkel and Jacques Kallis to share the new ball.
Pakistan: Misbah-ul-Haq (captain), Taufiq Umer, Mohammad Hafeez, Younis Khan, Umar Akmal, Azhar Ali, Saeed Ajmal, Abdul Rehman, Adnan Akmal, Umar Gul, Wahab Riaz
South Africa: Graeme Smith (captain), Hashim Amla, Johan Botha, Mark Boucher, AB de Villiers, Paul Harris, Jacques Kallis, Morne Morkel, Alviro Peterson, Ashwell Prince, Dale Steyn
Umpires: Asoka de Silva (SRI) and Daryl Harper (AUS)
TV umpire: Ahsan Raza (PAK)
Match referee: Andy Pycroft (ZIM)
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