This follows the resignation of the Commission's head Shan Ramburuth last year amid an investigation into his fitness to hold office.
Briefing journalists in Pretoria on Monday, 19 May, Patel said he was pleased to announce the appointment of someone of Bonakele's calibre.
Bonakele has acted in the position since October last year.
"I am pleased to have someone of Bonakele's calibre at the helm of the Competition Commission.
"He is taking leadership of the Commission at a time when the South African economy needs to become more competitive and create many more decent work opportunities by combatting market abuse such as cartels and pervasive monopolies and ensure competitive pricing of products.
"In particular, the key jobs drivers identified in our policy frameworks require coordinated and concerted efforts to improve economic performance and development outcomes.
"The Competition Commission has been one of a number of successful economic agencies and regulators that are together beginning to transform the South African economy. Mr Bonakele possesses the skills and experience to build on the successes of the Competition Commission."
Bonakele has been with the Commission for about 10 years.
He has been in its management team since 2006, and a Deputy Commissioner since 2008.
He played a key role in the establishment of the Commission's cartels division and has worked on most of the Commission's major cases over the past ten years, including the bread and flour cartel as well as the construction bid-rigging cartel cases, Telkom and SAB abuse of dominance cases and a number of other high-profile mergers.
He has been involved in negotiating a number of the Commission's ground-breaking settlements and helped develop the Commission's Corporate Leniency Policy as well as the Construction Fast Track Settlement Policy.
Bonakele welcomed his appointment.
"I am honoured and privileged to serve in such a wonderful institution. I am aware of the enormous task of leading the Commission and am committed to work with my colleagues to firmly establish the Competition Commission as an important institution in promoting economic development in South Africa."
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