Elsewhere in the Padres' system, Triple-A El Paso suffered a 17-5 loss to Tacoma and high Single-A Lake Elsinore was beaten 12-2 by Modesto. Both teams are 1-1 after the home losses. Low Single-A Fort Wayne had its Season Opener rained out a second straight day in Midland, Mich.
Right-handed starter Rea allowed seven hits over seven innings. He struck out six and didn't issue a walk. The left-handed Alger struck out two in two perfect innings to get the win.
Gonzalez walked to open the ninth, moved to second on a two-out single by Diego Goris and scored on the error. The Missions had only three hits.
Designated hitter Tommy Medica gave El Paso a 3-0 lead with a three-run homer in the bottom of the first against Tacoma. Medica finished 3-for-4 with a double and his first homer. Catcher Austin Hedges was 1-for-3 with a RBI double.
But Tacoma had 20 hits against the Chihuahuas pitchers. Right-handed starter Aaron Northcraft allowed seven runs on eight hits and a walk in 1 2/3 innings. Right-handed reliever Stephen Kohlscheen allowed six runs (three earned) in 2 1/3 innings.
Right-handed, Lake Elsinore starter Zechariah Lemond allowed two runs on six hits and a walk with seven strikeouts over six innings and departed with the game tied 2-2. But right-handed reliever Matthew Shepherd gave up seven runs on five hits and a walk in just two-thirds of an inning.
Third baseman Gabriel Quintana was 2-for-4 and gave the Storm a 2-0 lead in the first with a two-run single. Catcher Ryan Miller had two doubles in four at-bats and shortstop Jose Rondon was also 2-for-4.
Lake Elsinore enters the California League season with two pitchers and two outfielders selected by the Padres in last June's draft.
Lemond (the Padres' third-round pick) and Opening Day starter Ryan Butler (seventh round) are two of 13 pitchers on the Lake Elsinore roster. Center fielder Auston Bousfield (fifth round) and Yale Rosen (11th round) are two of the five outfielders on the 26-man Storm roster.
All four are college products. Lemond played at Rice University, Butler is a product of North Carolina-Charlotte, Bousfield went to Mississippi State and Rosen went to Washington State.
Other key players for the Storm are Rondon and infielder Fernando Perez from Otay Ranch High.
Lake Elsinore, which reached the California League playoffs in 2014 for the 12th time in 14 seasons, will be managed by Michael Collins. Rod Barajas is the hitting coach and Glendon Rusch is the pitching coach.
A native of Australia, Collins managed the low Single-A Fort Wayne TinCaps last season. Former Major Leaguers Barajas and Rusch are also in their first seasons with Lake Elsinore.
Lake Elsinore plays at the 6,066-seat Diamond, which is just over a hour's drive north of San Diego.
Rondon, 21, was the California League Rookie of the Year in 2014 while splitting time between Inland Empire and Lake Elsinore -- where he hit .301 in 37 games after coming to the Padres' system as part of the trade that sent closer Huston Street to the Los Angeles Angels of Anaheim.
Perez, 21, hit .284 with 18 homers and 95 RBIs last season. He led the Midwest League and the Padres' organization in RBIs. First baseman Marcus Davis, 22, hit .322 with seven homers and 31 RBIs in 60 games with short-season Single-A Eugene last season.
Bousfield, 21, hit .301 in 45 games with Eugene with 12 steals and a .404 on-base percentage. Rosen hit .247 in 54 games with seven homers and 29 RBIs. The Storm outfield will include Jeremy Baltz, 24, who hit .241 with 12 homers and 57 RBIs for Lake Elsinore last season, and Nick Schulz, 23, who hit .341 with eight homers and 30 RBIs in 49 games for Fort Wayne.
Butler was 1-1 with 10 saves and a 0.83 earned run average with Fort Wayne. Lemond was 2-3 with a 3.79 ERA in 11 games (eight starts) with Eugene.
The Lake Elsinore roster:
Pitchers (14): Kyle Bartsch (L), Ryan Butler, Rafael De Paula, Luis Hernandez, Ronald Herrera, Sam Holland, Zechariah Lemond, Justin Livengood, Kyle Lloyd, Nick Mutz, Dennis O'Grady, Matthew Shepherd, Walker Weickel and Eric Yardley.
Catchers (3): Ryan Miller, John Nester, Adolfo Reina.
Infielders (5): Reynaldo Bruguera, Marcus Davis, Fernando Perez, Gabriel Quintana and Jose Rondon.
Outfielders (5): Jeremy Baltz, Auston Bousfield, Kyle Gaedele, Yale Rosen and Nick Schulz.