Third seed Williams, chasing her seventh title at Flushing Meadows, got past Greek 15th seed Maria Sakkari in three sets, 6-3, 6-7 (6-8), 6-3.
The two were evenly matched but Williams got her advantage on second serve, winning 63% on her second compared to Sakkari’s 51%.
Williams also converted three of her eight break points, while regularly denying Sakkari who only managed one break from six opportunities.
The US Open favourite had served for the match in the second set but Sakkari rallied to level and win the tiebreaker to send it to a third set.
Only last week, Sakkari had stunned Williams at the Western & Southern Open but the American shook off fears of a repeat and finished the job.
“Of course I thought about it, but ever so little because it’s a completely different match and a completely different moment here,” Williams said when asked about their previous encounter.
“I just kept fighting. She was doing so well and being so aggressive, I just knew I had to do the same thing.”
The 23-time Grand Slam winner will next play Bulgarian Tsvetana Pironkova in the last eight.
This year’s Australian Open winner Kenin won’t be in the quarters after her straight sets loss to 16th seed Elise Mertens who’ll play two-tie US Open finalist Victoria Azarenka in the final eight.
In the men’s singles on Monday, second seed and new tournament favourite Dominic Thiem booked his place in the quarter-finals with a straight sets win over Canada’s Felix Auger-Aliassime.
Thiem will play Australian 21st seed Alex de Minaur who got past Vasek Pospisil, while Russian pair Daniil Medvedev and Andriy Rublev both won to set up a quarters meeting.