His unbeaten 104 guided the home side to 250 for five after Waqar Younis put them in. Off spinner Saqlain Mushtaq, meanwhile, claimed his 200th test wicket despite a tough day in the field.
Kallis faced 220 balls, his three-hour knock including 11 fours and a six, and featured in partnerships of 122 for the third wicket with opener Gary Kirsten and 55 for the fifth with Neil McKenzie.
Kirsten scored 56, while paceman Waqar took two for 54.
Kirsten and Kallis began their partnership after South Africa had slipped to 33 for two in the ninth over.
Graeme Smith was out in the sixth over for 16 when he pushed forward to a delivery from fast bowler Mohammad Sami and edged it to Kamran Akmal, who held a good low catch.
Three overs later, Herschelle Gibbs lazily slashed a ball from Waqar to Faisal Iqbal at backward point.
"I've had plenty of starts here and scored 60s and 70s, and it's great to get a hundred on one of the bounciest pitches in the country," Kallis said.
"The ball did something all day and reversed a lot, so you never felt in.
"If we can eke out 400 we'll be in a good position."
Just before tea, Saqlain claimed two wickets in two overs to reach his 200 wickets and end the day with two for 87.
Kirsten failed to control a quicker delivery and flighted the ball to Younis Khan before Boeta Dippenaar cut expansively at a wide delivery and was caught off the bottom edge.
The match started 40 minutes late because of rain, and play ended 14.3 overs early due to bad light.
The visitors, beaten 4-1 in the one-day series, opted to bolster their batting by selecting Faisal Iqbal at seven.