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The 20-year-old caused an upset in Melbourne when she came from a set down to beat the world number one 3-6 7-5 6-4, but there was to be no repeat in New York as Williams advanced to the quarter-finals of the US Open.
All the talk before the match was of a possible rift between the two Americans, and it was the more experienced of the pair who rose to the occasion.
Williams made the breakthrough to go 4-3 ahead, but she suffered a double fault when facing a break point in the next game and gifted it right back to Stephens.
The five-time champion, who is also looking for back-to-back titles in New York, did not let that deter her, as she broke decisively to take the first set 6-4.
The 31-year-old stepped through the gears in the second set, blowing her opponent away 6-1 to set up a meeting with Carla Suarez-Navarro in the last eight.