Bulc was appointed deputy prime minister on 2 October but will now travel to Brussels to meet commission president-elect Jean-Claude Juncker. A spokesperson for the European Commission said the pair will meet "early next week".
It has not been confirmed whether Bulc will take over Bratusek's place as vice president for energy union or if there will be a reshuffle among Juncker's team. A reorganisation could delay the new commission from taking office on 1 November.
Bulc is a entrepreneur, having set up Vibacom, a company which advises businesses on growth strategies and employee development.
She entered the Slovenian coalition government on 18 September as minister without portfolio responsible for development, strategic projects and cohesian before being promoted to deputy prime minister.
In a vote by the environment and energy committees, 112 MEPs opposed Bratusek's candidacy, with just 13 votes in favour and two abstentions.
Bratusek was criticised for her performance when questioned by the committees on Monday. MEPs said she appeared ill-prepared and unable to explain the concept of an energy union.
The committees accepted Miguel Arias Canete as climate and energy commissioner with a 77 to 48 vote in favour of the Spaniard.
The European Parliament will vote to accept or reject Juncker's commission on 22 October.