The 19-year-old Canadian teamed up with Williams to win a doubles match on Tuesday as the 44-year-old American great returned to action after almost four years away from the sport.
Having beaten third seeds Nicole Melichar-Martinez and Erin Routliffe they were scheduled to face Leylah Fernandez and Laura Siegemund in the quarter-finals on Thursday.
Mboko, trailing 6-2, 3-4 to the powerful Czech player, had a break point but fell awkwardly on the slick grass behind the baseline as she tried to change direction.
After being helped to the net she looked uncomfortable and emotional and opted to retire.
Earlier on a showery day at the pre-Wimbledon tournament, second seed Amanda Anisimova breezed past Germany's Laura Siegemund 6-1, 6-3 to set up a quarter-final against fellow American Iva Jovic who easily beat Alexandra Eala 6-2, 6-2.