Stubbs was unbeaten 68 while Tony de Zorzi struck 55 as the visitors dug in for the final two sessions after wrapping up the Pakistan innings before lunch.
It was a first fifty plus score for Stubbs in the longest format since scoring a hundred against Sri Lanka in Durban in November 2024.
Keshav Maharaj was the destroyer-in-chief for the Proteas with the ball, finishing with figures of 7-102 in 42 overs after the home team resumed on 259-5.
The left-arm spinner picked up both overnight batters, Saud Shakeel (66) and Salman Agha (45), before ripping through the tailenders to get the tourists batting before the lunch interval.
Aiden Markram and Ryan Rickelton survived a tricky period but the latter was out caught behind to seamer Shaheen Afridi for 14 to leave the Proteas on 22-1.
Markram was joined in the middle by Stubbs and made his way to 32 but gave it away when he holed out to long-on to the bowling of spinner Sajid Khan.
Stubbs and DeZorzi then dug in and combined for partnership of 113 for the third wicket, taking the score from 54 to 167.
Just as it looked as the Proteas would end the day in a strong position, Pakistan's 38-year-old debutant spinner Asif Afridi struck a double blow.
The left-arm slow-bowler first trapped De Zorzi lbw, given out on review, before Dewald lasted just four balls before edging to slip for a duck.
Kyle Verreynne was 10 not out and together with Stubbs will look eat into the deficit as the Proteas look to square the two-match series.
The Proteas Women made it five consecutive victories at the ICC Women's World Cup after a comprehensive 150-run win (DLS method) against Pakistan in match that was shortened due to rain.
The Proteas fought back with two late wickets but will rue a few missed opportunities as Pakistan were 259-6 at stumps on the first day of the second Test in Rawalpindi.
The Proteas Women have secured a spot in the ICC Women's World Cup semifinals after the game between New Zealand and Pakistan was abandoned because of rain in Colombo.
Temba Bavuma has been included in the South Africa A side for a first-class fixture next month to prove his fitness ahead of the Proteas' Test series in India.
