The departure was reported to be amicable and over "creative differences", but sources say that Jenkins was fired without warning, according to The Hollywood Reporter.
Portman - who recommended Jenkins for the role - was reportedly already considering her involvement in Thor 2, wanting to spend more time with her baby, and is said to have re-engaged with the project following Jenkins's appointment.
The appointment would have made Jenkins the first female director to helm a major superhero film.
Portman is contractually obligated to appear in the film, and Marvel is seeking to smooth over her issues by involving her in the search for a replacement director.
Game of Thrones directors Daniel Minahan and Alan Taylor are rumoured to be under consideration as Jenkins's replacement.
Chris Hemsworth and Tom Hiddleston are both confirmed for the sequel.