The top-order batsman smashed 79 to help his team surpass South Africa's modest total of 199 with more than five overs to spare in a match which was held up for nearly 10 minutes in the morning due to poor pitch conditions.
Pakistan coach Bob Woolmer and South Africa captain Graeme Smith came onto the ground and were involved in mid-pitch discussions with umpires Peter Parker and Ian Gould after players complained of the pitch which had a variable bounce.
The incident came just a few days after a sightscreen had collapsed during the Pakistan-Canada practice game at the same venue, halting play for more than an hour.
"It was a tale of two pitches. When we batted it was wet and difficult, but later the pitch dried up and became easier," said South African coach Mickey Arthur, whose side were put in to bat.
"It took us another 10 overs after the halt to get into the groove. There's absolutely no panic. These are just practice games and I hope we do well when the main competition starts."
Younis showed there were no demons in the track as he batted with authority against the South African attack, hitting one six and nine fours in his impressive 98-ball knock.
Younis was not the only Pakistani batsman among runs as opener Mohammad Hafeez scored a stylish 49 to put his team on course for an emphatic victory. The pair put on 68 for the second wicket.
Mohammad Yousuf also gained valuable batting practice ahead of his team's opening World Cup match against the West Indies at Jamaica on March 13, scoring a fluent 48 not out. He put on 100 for the third wicket with Younis.
"I am delighted that all my batsmen and bowlers have got some good practice. This is an ideal time to enter the main competition," said Pakistan skipper Inzamam-ul-Haq.
"Definitely, the (batting) conditions were not good in the first innings. A few balls did cause some problems. Batting first was difficult."
South Africa were not so fortunate as their batting left a lot to be desired in the second successive match. They managed just 192 against debutants Ireland in their opening game after being reduced to 91-8 at one stage.
They failed to solve their batting problems against Pakistan as only Loots Bosman gave a good account of himself with a solid 53 against the pace-spin combination.
Pakistani seamers Mohammad Sami and Umar Gul, and off-spinners Hafeez and Shoaib Malik grabbed two wickets apiece.
South Africa's total owed much of its substance to Bosman, who defied the Pakistani bowlers with a sensible 57-ball knock which included one six and four boundaries.
South Africa's hopes of gaining valuable batting practice ahead of the World Cup suffered a setback when they lost openers Smith and AB de Villiers with just five runs on the board.
They were reeling at 27-3 when Herschelle Gibbs departed after making 11, but Jacques Kallis (29) and Ashwell Prince (35) steadied the innings with a 66-run stand for the fourth wicket.
Bosman held the innings together after early blows, but South Africa's final total was too small to put pressure on Pakistan.
South Africa are in Group A with Australia, the Netherlands and Scotland, while Pakistan are in Group D with the West Indies, Ireland and Zimbabwe. The top two sides from each group will advance to the next Super Eight stage.
Fall of wickets: 1-5 (de Villiers), 2-5 (Smith), 3-27 (Gibbs), 4-93 (Prince), 5-93 (Kallis), 6-136 (Boucher), 7-173 (Pollock), 8-183 (Bosman), 9-194 (Hall).
Fall of wickets: 1-7 (Nazir), 2-75 (Hafeez), 3-175 (Younis).
Result: Pakistan win by seven wickets