Amla struck 92 off 128 balls before he was out attempting to cut a wide delivery from Rahat Ali and got a faint edge through to wicketkeeper Sarfraz Ahmed.
AB de Villers (40) and Robin Peterson (two), fresh from an 84 in the last Test in Cape Town, will resume after the interval.
Rahat, with figures of 3-57, has helped put Pakistan in the ascendancy after Amla and Faf du Plessis got South Africa back on track following a poor start.
Openers Graeme Smith (five) and Alviro Petersen (10) both struggled early on as Pakistan's bowlers used the seamer-friendly conditions to their advantage inside the first hour.
Petersen's miserable series continued when he was trapped plum lbw by Rahat, who returned to the side after missing the second Test in Cape Town.
Smith battled for 47 minutes to reach five before he became debutant Ehsan Adil's first wicket in Test cricket with just the third ball of the seamer's spell when a touch of away movement found his edge and looped towards Younus Khan at second slip.
Du Plessis (29) came in at number four in the place of Kallis and after a slow start crashed three boundaries off one Adil over to get his innings up and running.
Adil got his revenge after lunch though, inducing an edge to Sarfraz after the batsman advanced down the track to the medium pacer.
It ended a partnership of 69 between Amla and Du Plessis that helped the hosts recover from 38 for two early on.
De Villiers put on 79 with Amla before the latter fell and shortly afterwards Dean Elgar (seven) was trapped lbw by Rahat.
South Africa had weakened their batting line-up by replacing the injured Jacques Kallis with debutant swing bowler Kyle Abbott, elevating Peterson up to number seven.
South Africa lead the three-match series 2-0 having won the first Test in Johannesburg by 211 runs, before completing the series win with a four wicket victory in Cape Town.