Kerr and Lloyd's moves were part of a blockbuster trade also involving US national team striker Christen Press, the three huge stars of the women's game stealing the headlines on draft day as they rotated between clubs to replace each other, according to American media.
Lloyd will take Kerr's place Sky Blue, returning to her home state of New Jersey, Press will replace Lloyd at Houston Dash, and Kerr will move into Press' spot at Chicago Red Stars.
Reigning league MVP and golden boot winner Kerr was the standout player in the NWSL last season, breaking the all-time goal-scoring record in the league with 37 goals and becoming the first in the NWSL to score four goals in one game.
She also had an incredible year back home - claiming Australian Sportswoman of the Year, ABC Sports Personality of the Year, the W-League's Julie Dolan Medal, Asian Player of the Year, and being named in the IFFHS World Team of the Year.
The draft saw Stanford's Andi Sullivan, already a USA international, go to Washington Spirit as number one pick.
The mammoth three-club deal is also said to involve a large number of other picks and players to be announced later. Canada international Janine Beckie is also reportedly involved.
Here is what each club will reportedly get overall:
Sky Blue: Lloyd, Beckie, another player yet to be announced, draft pick no. 6 and pick no. 13
Chicago: Kerr, Nikki Stanton and pick no. 24
Houston: Press, an international roster slot and pick no. 7