Play was suspended just before 1pm local time because of the threat of lightning and rain quickly followed.
Only a few minutes of play were possible over the next four hours and at 5.10pm organisers announced several women's matches had been cancelled.
With a third of the men's first-round matches still to be played, they took priority over the women starting their second round, which included both Williams sisters.
Venus had just started her match against Zheng Jie so was allowed to try to complete it but Serena, who had been due to take on Galina Voskoboeva, was taken off the programme for Arthur Ashe.
That meant the night session, featuring the first match of his title defence for Andy Murray, had a chance of starting close to the scheduled time of 7pm.
Eighth seed Angelique Kerber, ninth seed Jelena Jankovic and Wimbledon runner-up Sabine Lisicki also had their matches cancelled along with Martina Hingis, who was due to partner Daniela Hantuchova in the doubles in her first grand slam match for six years.
The two happiest players were Li Na and Agnieszka Radwanska, who beat the rain to reach the third round.
Third seed Radwanska had a tough second set against Maria-Teresa Torro-Flor but came through 6-0 7-5 while fifth seed Li defeated Sweden's Sofia Arvidsson 6-2 6-2.
Li said: "I was so lucky before the rain came that I finished the match so I don't have to wait and warm up and come to the court again. It is tough for (everyone else).
"For me, I'll just relax for the rest of the day and do whatever I want to do."
Li could play 30th seed Laura Robson in the third round in a repeat of last year's clash at the same stage, which was won by the British teenager.
Robson was just about to start her clash with France's Caroline Garcia when play was stopped.
Meanwhile, Flushing Meadows was still buzzing from the performance of 17-year-old Victoria Duval, who upset former champion Sam Stosur under the lights on Tuesday night.
The teenager grew up in Haiti, where she was once held hostage as a seven-year-old, but moved to America to further her tennis and plays for the US.
Duval was cheered on by a whole section of family and friends, including her father, Jean-Maurice.
A doctor in Haiti, he almost died in the devastating 2010 earthquake and has been unable to work since.
Duval is ranked 296th in the world and came through qualifying to reach the main draw, and she hopes her run here will make life easier.
She said: "It was definitely financially difficult, especially after the earthquake. My dad wasn't able to work any more.
"I've been very fortunate. A couple of family members have helped me. Hopefully with this win, that will change a little bit."
Most importantly for Duval, her father, who now lives in Canada, is on the mend.
She said: "He's improving so much. Emotionally it was hard at first but he's as happy as he's ever been. He had a couple of surgeries that helped take the pain away.
"We're just so happy that he's in a good state of mind right now. He's just here with us so it's incredible."