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SAN DIEGO -- It was the kind of matchup that only an extra-inning marathon can produce -- an infielder pitching to a batter working on an 0-for-6 afternoon, including four strikeouts.

With the Petco Park lights on as dusk fell, Mark Reynolds hit a three-run homer off infielder Josh Wilson with two outs in the 18th inning, sending the Arizona Diamondbacks to a 9-6 win over the San Diego Padres on Sunday in the longest major league game this season.

"It's tough because No. 1, he's a position player and you don't want him to get you out, and No. 2, you don't know what he's going to throw," Reynolds said.

The Padres were held hitless through nine extra innings by four relievers. Their only baserunners in extras came on three walks. The game took 5 hours, 45 minutes.

San Diego used all its relievers and had starter Chad Gaudin -- the loser in Friday night's series opener -- pitch the 16th and 17th innings before turning to Wilson in the 18th for his third career relief appearance.

Wilson (0-1) was claimed off waivers from Arizona on May 15, four days after he pitched a scoreless inning for the Diamondbacks against Cincinnati.

"When he pitched for us he threw all fastballs, so you figure he has some kind of wrinkle," said Reynolds, who fell behind 0-2. "He threw a curveball up there and I laid off some high fastballs, and he left one out over and I was able to barrel it up."

Wilson allowed a single to Felipe Lopez and walked Ryan Roberts with one out before Reynolds hit a full-count pitch off an advertising sign atop the right-field wall.

"One pitch away," Wilson said. "I had Mark 0-2 there. I wish I could have thrown a strike before I got to 3-2.

"I was very comfortable," he added. "I expected it in that type of game. It was probably just a matter of time. I was ready."

Wilson pitched in high school and his two other big league relief appearances had been in blowout losses.

"I don't know how long I could have lasted," he said. "I started getting tired toward the end of that inning."

Arizona manager A.J. Hinch said he didn't want his players getting comfortable facing a position player.

"Your swings can get a little bit big," said Hinch, who had Gerardo Parra lay down a sacrifice bunt to advance Lopez. "We had the players concentrate on getting a good pitch to hit and hit it hard."

Hinch said he had his pitching figured out for at least 22 innings before he would have to go to a position player.

Padres manager Bud Black said he didn't want to overextend Gaudin.

San Diego scored five in the ninth and tied it at 6 on David Eckstein's first career pinch-hit homer, a three-run shot with two outs off Chad Qualls.

Leo Rosales (1-0) pitched 3 1/3 innings for the win.

It was the longest big league game by time and innings since San Diego beat visiting Cincinnati 12-9 in an 18-inning game that lasted 5 hours, 57 minutes on May 25, 2008, according to the Elias Sports Bureau.

Eckstein hit a first-pitch fastball from Qualls off the balcony on the second level of the Western Metal Supply Co. brick warehouse in the left-field corner. It was his first homer in 217 at-bats since Sept. 17 with Arizona.

The 5-foot-7 Eckstein, MVP of the 2006 World Series with St. Louis, has 33 homers in his nine-year career.

It was the third time the Diamondbacks played an 18-inning game.

The Padres have played the two longest games in the majors this year. They beat Cincinnati 6-5 in 16 innings on May 16, taking 5 hours, 14 minutes.

Stephen Drew had four hits for Arizona, extending his hitting streak to 11 games.

Arizona's Dan Haren held San Diego to one run and four hits in seven innings, retiring 13 straight batters during one stretch. Haren's only mistake was allowing Kevin Kouzmanoff's homer with two outs in the seventh.

The Diamondbacks overcame three early baserunning blunders. Josh Whitesell hit a three-run double off Josh Geer in a four-run fifth.

Game notes

Diamondbacks OF Justin Upton left with an aggravated left shoulder after striking out in the 10th. ... Padres slugger Adrian Gonzalez extended the club record by walking at least twice in six straight games. Gonzalez has walked six times in the first three games of this four-game series, 13 times in the last six games and 17 times in the last nine. ... It was Qualls' third blown save in 15 chances.