With the Padres trailing 3-2, Alonso drove a 2-2 pitch from Miley (2-1) into the Jack Daniel's Old No. 7 deck in right-center, his fourth. It would have been a home run even in Petco Park's old configuration. The fences were moved in 11 feet from the home run porch in the right-field corner to the gap in an attempt to make the downtown ballpark play fairer. Jesus Guzman was aboard on a grounder.
The homer made a winner of Jason Marquis (3-2). Marquis allowed three runs and four hits in six innings, struck out five and walked five.
Huston Street came on with runners on first and second and no outs in the ninth and retired two batters before allowing Gerardo Parra's three-run homer to straightaway center, his second. Street then got Martin Prado to fly out to center for his seventh save in as many chances.
Padres rookie Jedd Gyorko had his first three-hit game, including two doubles.
Miguel Montero homered to straightaway center field off Marquis leading off the second, his second.
San Diego took a 2-1 lead in the bottom of the inning on Gyorko's leadoff double and, with two outs, a single by Chris Denorfia and a triple by Everth Cabrera.
The Diamondbacks regained the lead in the fourth on an RBI double by Eric Chavez and a run-scoring groundout by Cliff Pennington.
The Padres added on in the seventh and eighth. Guzman doubled to right-center and scored on Kyle Blanks' single in the seventh. In the eighth, Cabrera's sacrifice bunt brought in a run and Chase Headley hit an RBI double.
Miley, who finished second to Bryce Harper in NL Rookie of the Year balloting last year, allowed four runs and nine hits in five innings, struck out four and walked three.
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