On the night the Yankees lost Derek Jeter until after the All-Star break, they also lost their series finale against Arizona. The Yankees wasted Phil Hughes’ bounce-back start, squandered Francisco Cervelli’s game-tying ninth-inning homer, as David Phelps’ dismal outing dooming them to a 6-2, 12th-inning defeat last night at the Stadium. Phelps loaded the bases and allowed Cody Ross’ go-ahead RBI single and gave up a bases-clearing double to ex-Yankee Eric Chavez. After the Yankees suffered through the news of Jeter’s fractured left ankle — one that will cost him at least three months — it was a gloomy end to what was shaping up as a solid homestand. “I’ve got to make better pitches with men on base,’’ said Phelps (0-1), who found it difficult to overcome leadoff doubles in both the 11th and 12th. “Difficult is a great word, especially in an extra-inning game. They’re looking to score one run: A bunt and a sac fly they score a run. You’ve really got to get to making pitches right away. I’ve just got to make better pitches; that’s what it boils down to.’’ Manager Joe Girardi said Phelps was falling behind hitters, and he had done so in the 11th as well, wiggling out of a two-on, none-out jam by retiring AJ Pollock, Didi Gregorious and Eric Hinske. There would be no encore for Phelps in the 12th. Leadoff hitter Gerardo Parra doubled over Ichiro Suzuki’s head in right, and Cervelli committed his second catcher’s interference of the night to put Paul Goldschmidt on.