Khurram Manzoor was unbeaten on 41 and with him debutant Shan Masood was on a confident 36 as Pakistan trail South Africa's first innings total of 249 by 172 runs.
Both Pakistani openers negotiated a four-pronged South African pace attack without any trouble on a Sheikh Zayed Stadium pitch which had little on offer for the fast bowlers.
Khurram, playing his 10th Test, has so far hit four boundaries while Masood, a prolific scorer in Pakistan's domestic matches, has also hit as many boundaries.
Earlier, Mohammad Irfan (3-44) dismissed centurion Hashim Amla off the second ball of the day after South Africa had resumed at 245-8.
Amla, who made 118, edged a sharp Irfan delivery straight into the hands of slip where Younis Khan held a regulation catch. He hit 13 boundaries off 252 balls and anchored the South African innings on Monday.
Debutant left-arm spinner Zulfiqar Babar took 3-89 while Saeed Ajmal had figures of 2-59.
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