Williams chose Mboko to play alongside her at Queen's and they opened the 44-year-old sporting great's first outing in nearly four years with a win at London's Queen's Club on Tuesday.
But a left medial collateral ligament (MCL) injury sustained by the teenager in her opening singles match the following day forced the her to retire initially from that competition.
The 19-year-old then pulled out of the doubles on Thursday morning, followed by an announcement on Friday that she would miss Wimbledon and the remainder of the grass-court season.
Posting to her Instagram on Friday morning and tagging in 23-time Grand Slam singles winner Williams, Mboko wrote: "Thank you Serena Williams for giving me this incredible opportunity to play alongside you.
"I learnt so much from you and am so sorry our tournament came to an end prematurely, but I hope we can play together again soon and finish what we started."
Williams next turns to Berlin, where – even before Mboko's injury – she had elected to partner Karolina Muchova.
The 23-time grand slam singles champion has danced around the idea of a London return at Wimbledon, where she won seven individual titles and six doubles titles alongside sister Venus.
Wimbledon's wildcard committee will formally make their decisions next week.
