Sinner, whose coach said he was “physically and mentally” worn down by the investigation, found himself a set and a break down after a poor start on Arthur Ashe Stadium.
But he found his footing midway through the second set and it was plain sailing from there for the 23-year-old.
Sinner said the overall response to news that he had tested positive twice for a banned substance was “not bad”.
“The response from fans, I feel it has been great – throughout when the news came out, in the practice sessions, there was a lot of support, which I’m very glad and happy about that,” Sinner said in a news conference.
Asked about the reaction from other players he said: “I cannot control the players’ reaction, and if I have something to say to someone, I go there privately, because I’m this kind of person.”
Alcaraz, by contrast, started strongly, quickly finding himself a set and a break up before the unforced errors started to creep up.
However, he readjusted well in the third set and was dominant in the fourth, finishing with 50 winners to his opponent’s 19.
Alcaraz is bidding to become the third man in history after Rod Laver and Rafael Nadal to win the French Open, Wimbledon and the US Open in the same calendar year.
When asked about the statistic on ESPN, he joked: “Well, after this interview I’m going to try to pretend I never heard that.
“Obviously it would be a great achievement if I make it, but it is going to be difficult.”
He and Sinner are the favourites to challenge defending champion Novak Djokovic, who beat Alcaraz just three weeks ago to clinch Olympic gold.