Hughes tossed 6 2/3 strong innings and combined with three relievers on a four-hitter as the Yankees blanked visiting Rochester, 3-0, on Sunday.
"It was a step in the right direction," the former first-round pick said. "Everything got better. I was happy overall."
In his fifth rehab start, Hughes (4-1) gave up three hits and three walks, striking out four while tossing 91 pitches in his longest outing of the season.
"It's good to get up around the seven-to-eight-inning, 90-pitch mark. That was my goal," he said. "It wasn't my best, but it was close. Overall my stuff was pretty good."
The 21-year-old right-hander, who had injured his hamstring and left ankle in the Bronx, has kept opponents scoreless in his last 16 1/3 innings. He combined on a two-hit shutout in his last rehab start Tuesday against Louisville.
"Physically, I felt great," he added.
"He did what he needed to do," pitching coach Dave Eiland said. "He worked on some things, but the young man is ready to move on."
Edwar Ramirez struck out the final batter in the seventh inning, and Ross Ohlendorf allowed a hit and a walk while fanning one in the eighth. Jose Veras tossed a perfect ninth to notch his first save and seal the Yankees' 10th shutout.
Angel Chavez stroked a two-run single in the first and Andy Cannizaro lifted a sacrifice fly in the fifth for Scranton/Wilkes-Barre (59-46).
Red Wings starter Ryan Mullins (0-2) surrendered three runs on six hits and a walk with three strikeouts over six innings.
Alexi Casilla, Garrett Jones, Chris Heintz and Denard Span each had a base hit for Rochester (58-51).