The prize - the UN's highest environmental accolade - is awarded to leaders from government, civil society and the private sector whose actions have had a significant and positive impact on the environment.
Potočnik, 55, will receive the prize for policy leadership in promoting resource efficiency and combating food waste.
Potočnik has called for EU member states to pursue policies and incentives to promote sustainable consumption and production, most notably in the agricultural sector, said a statement from the United Nations Environment Programme (UNEP), which awards the prize.
"It is an honour to receive this award and I wish to express to UNEP my deep appreciation for its work on sustainable development," Potočnik said. "Unless we change the way we produce and consume we will face a crisis in our natural resources. It is crucial that we make the necessary changes now rather than when we hit environmental tipping points."
Since Potočnik took office in 2010, the EU has set targets to halve food waste and nearly eliminate landfill by 2020.
Earlier this year, he even offered to write and sing a ditty in front of 1,000 people - if the same number could be persuaded to leave their cars at home for a day. Unfortunately, they could not.
UNEP Executive Director Achim Steiner said: ”Despite the challenges posed by the financial crisis and the economic downturn Mr. Potočnik played a key role in maintaining Europe's focus on the future as an advocate for a more sustainable and resource efficient economy. Science, innovation and persistence have been leitmotifs of his tenure as Commissioner for the Environment."
Google Earth, Slow Food Movement founder Carlo Petrini, and Izabella Teixeira, the Brazilian environment minister, have previously been awarded the prize.