Sefcovic had been previously nominated to be the commissioner for transport in the incoming commission led by Jean-Claude Juncker.
Juncker was forced to reshuffle his team after former Slovenian Prime Minister Alenka Bratusek was rejected by the environment and energy committees for the vice president role after a heavily-criticised hearing.
Following the announcement, Sefcovic tweeted he was "fully conscious" of the challenges of the energy portfolio, adding, "Reducing energy dependency, ensuring connectivity, reducing emissions important for boosting EU competitiveness."
Sefcovic is commissioner for inter-institutional relations in the current Jose Manuel Barroso commission.
Bratusek's replacement is Violeta Bulc, deputy prime minister in Slovenia, will now take the transport role.
Both Sefcovic and Bulc will need to face questions from MEPs before being confirmed which could delay the final vote for the full commission, which was due to take place 22 October.