Shortland, 49, is best known for the Nazi drama "Lore" and most recently directed Teresa Palmer-starrer "The Berlin Syndrome".
According to The Hollywood Reporter, the studio met with over 70 directors to find the right person to helm the project.
Its hunt narrowed down to Amma Asante, Maggie Betts, Shortland, Melanie Laurent and Kimberly Peirce.
Shortland, who had a promising meeting with Johansson, later bagged the project.
In January, the studio had announced that Jac Schaeffer will be penning the script for the standalone.
Johansson has till now appeared as the character in seven films, including this summer's smash hit "Avengers: Infinity War".