But the ruling angered Pakistan Cricket Board chairman Najam Sethi, who said he will be contacting the International Cricket Council.
"PCB is writing a letter to the ICC, seeking explanation of inconsistency by match referee in application of ball tampering rule to Afridi vs. Faf," Sethi tweeted.
Pakistan allrounder Shahid Afridi was banned for two Twenty20 internationals for ball tampering during a one-day international against Australia in 2010.
Du Plessis is the first South African to be found guilty of ball tampering, but former Pakistan players criticized the ICC for showing him leniency.
"ICC can't do justice on merit, it doesn't have any guts to do so," former test fast bowler Shoaib Akhtar told Geo Television.
In 2003, Akhtar was fined 75 percent of his match fee and was also banned for two one-day internationals for ball tampering during a series in Sri Lanka in 2003.
"It's fine if he (du Plessis) got away with such a punishment, but if in the future any player is involved in rubbing the ball over a zip ... please do hand him a similar punishment and not more than that," Akhtar said.
Former captain Rashid Latif said du Plessis should have been suspended, and captain Graeme Smith should also have been punished.
"The punishment is very lenient," Latif said. "I think Faf should have been banned for six months ... plus the captain of the team should be held responsible and punished. I am surprised. ... They ban a captain on a minor offense for a slow over rate but for a crime shown on television in front of the whole world, you get a punishment of only 50 percent of the match fee."
Moosajee said Cricket South Africa was working on an ICC deadline of 2015 to make sure there's no zips on the clothing of the players, "especially the trousers."
"We have already begun the process and we will be making sure that we will meet this timeline," Moosajee said.
Pakistan's Waqar Younis was the first international player to be sanctioned for ball tampering when in 2000 he was fined 50 percent of his match fee and suspended from a one-day international. Allrounder Azhar Mahmmod is the other Pakistani who has been fined for ball tampering.
Other international players who have been handed fines, suspensions or both include India's Rahul Dravid and Sachin Tendulkar and England's Michael Atherton.
It's only the second time in the history of test cricket that five penalty runs were awarded to any team for ball tampering.
Pakistan was at the receiving end during the Oval test in 2006. Then Pakistan captain Inzamam-ul-Haq reacted strongly and decided not to continue the test in protest. Australian umpire Darrell Hair responded by awarding the game to England the only forfeit in test history.