"It has been a privilege working for an organisation that is at the core of infrastructure development," Jardine said in a statement.
"However, the Competition Commission's investigation process has been personally very taxing, particularly as I have had to deal with matters that occurred before my appointment and of which I had no personal knowledge."
Jardine's resignation would be effective from August 31. Financial director Kobus Verster would be acting CEO from September 1.
In June, 15 construction companies, including Aveng, agreed to pay fines that collectively totalled R1.46bn for collusive tendering.
The settlements were reached in terms of the "construction fast track settlement process" the Competition Commission started in February 2011. This process encouraged firms to make full and truthful disclosure of bid rigging in return for penalties lower than what the commission would seek if the cases were prosecuted.
Twenty-one firms responded to the offer and 300 instances of bid rigging were revealed. The settlements related to projects concluded after 2006. Projects before that were beyond prosecutorial reach.
The commission said the companies colluded to create the illusion of competition by submitting "sham tenders" or "cover pricing", to allow an alleged conspirator to win a tender.