SAN DIEGO -- Melvin Upton Jr. homered on the first pitch of the ninth inning thrown by New York left-hander Andrew Miller to give the San Diego Padres a 2-1 walk-off win over the Yankees on Saturday night at Petco Park.

It was Upton's third walk-off homer of the season.

Brad Hand (2-2) pitched a scoreless ninth to get the win. Miller suffered his first loss to fall to 5-1.

After a five-inning scoreless duel featuring pitchers Drew Pomeranz of the Padres and Ivan Nova of the Yankees, both teams scored in the sixth.

The left-handed Pomeranz allowed three hits and no walks in the first five innings as he extended his scoreless innings streak to 14. He had six strikeouts going into the sixth.

Nova also allowed three hits and no walks with seven strikeouts in the first five innings.

The Yankees got on the board first in the top of the sixth. Jacoby Ellsbury opened the inning with a line-drive double over the head of Matt Kemp in right and advanced to third when Brett Gardner was awarded an infield single when Pomeranz botched his attempt at a sacrifice bunt. Ellsbury scored on Castro's groundout to the right side.

But the Padres tied the score in the weird bottom of the sixth that included the second and third of three appeals that went against the Padres in the game.

Travis Jankowski opened the inning by hitting what appeared to be an opposite-field double to left. Jankowski was called safe at second. But Yankees manager Joe Girardi appealed and Jankowski was ruled out.

Wil Myers then drew a walk from Nova, who was immediately replaced by right-handed reliever Dellin Betances. Myers stole second and scored on Kemp's opposite-field double down the right-field line.

After Yangervis Solarte struck out for the second out, Melvin Upton Jr. singled to right. Yankees right fielder Rob Refsnyder threw a strike to catcher Austin Romine for the out.

The Padres appealed, but the call was upheld -- meaning the Padres scored one run on two doubles, a single and a walk in the inning while losing two appeals.

Pomeranz worked seven innings and allowed one run and five hits with seven strikeouts. Nova allowed his run on four hits and a walk with seven strikeouts in 5 1/3 innings.

NOTES: The Yankees placed RHP Conor Mullee on the 15-day disabled list and activated RHP Chad Green, who is scheduled to start the series finale on Sunday afternoon. Mullee came out of Friday night's game experiencing "a funny feeling" in his pitching hand. ... Although OF Carlos Beltran doubled as a pinch hitter Friday, he missed a second start in San Diego on Saturday night with hamstring tightness. ... Padres RHP Erik Johnson will be out three to six weeks after an MRI on Friday showed a strained flexor tendon. ... The Padres signed six of the top-30 and eight of the top-50 rated international prospects on the first day of the international signing period. Topping the list was Dominican Republic SS Luis Almanzar, who was ranked the No. 2 amateur prospect in Latin America.