Serena announced the news on social media alongside a video of herself limping with strapping on her right leg and pictures of large syringes of fluid drained from her knee.
"I'm heartbroken to have to withdraw from doubles. Coming back to compete again has been a gift, and the opportunity to play alongside @venuswilliams once more meant the world to me," the 44-year-old said on Instagram.
"I did everything I could, but unfortunately my knee just isn't ready to compete.
"The photo of the syringes is the fluid they drained from my knee after my singles match - yikes! The good news is that my knee shouldn't swell or collect that much fluid again.
"The bad news is that, as hard as I tried, I wasn't able to be ready for doubles."
The American's highly anticipated return to Grand Slam tennis after four years away ended in disappointment after a 6-3, 6-7(6), 6-3 defeat by Australian youngster Maya Joint on Tuesday.
The Williams sisters, who have six doubles titles at the All England Club, received a wildcard and were drawn to play Solana Sierra and Camila Osorio in the opening round this week.
Serena said after her defeat by Joint she had "tweaked" her right knee at the end of the first set but would do everything to be ready for action again.
"I'm especially grateful to tournament director, Jamie Baker, and the entire tournament team for giving me every opportunity to recover," Serena added.
"Thank you to the fans for your incredible support and for making this comeback so meaningful… All I can say is stay tuned to a city near you..."
Serena partnered Canadian teenager Victoria Mboko at the WTA event at Queen's Club last month, but the pair's campaign was cut short after Mboko's knee injury in singles action.
Serena then paired up with Czech Karolina Muchova in the Berlin Open, but the duo went down in their first match.