It was Hunter's first three-homer game in the majors. He was left on deck when Bobby Abreu struck out to end the bottom of the eighth inning, costing him a chance at tying the big league record for home runs in a game.
Hunter became the 12th player in Angels history to homer three times in a game, and the first to do it since Garret Anderson in 2003 against the Montreal Expos at Puerto Rico.
Hunter, who homered his first time up in Friday night's 11-6 win, put the Angels ahead 4-0 when he led off the third with a drive over the left-field fence.
The two-time All-Star, who tops the Angels with 16 homers and 49 RBIs, made it 5-0 in the fifth with a two-out drive. Center fielder Tony Gwynn Jr. made a valiant leaping attempt to pull it back, but the ball cleared his glove.
In the seventh, Hunter connected against lefty Joe Thatcher and was urged out of the dugout by the crowd of 43,233 to take a curtain call.
Hunter lined out in his first at-bat of the night.
Joe Saunders (7-4) came within two outs of his third career complete game and second this season. The left-hander allowed a run and eight hits, striking out five before manager Mike Scioscia lifted him after a season-high 113 pitches with two runners on base.
The first four Angels home runs came off Josh Geer (1-2), who gave up seven runs and nine hits in 5 2-3 innings. Padres ace Jake Peavy was scheduled to start, but was placed on the disabled list Saturday because of a strained tendon behind his right ankle. The 2007 Cy Young winner is expected to be out at least four weeks.
Geer was the second Padres pitcher in four games to give up four home runs. Chris Young did it last Tuesday in a 6-4 loss at Dodger Stadium.
One night after recording season highs with 11 runs and 18 hits against the Padres, the Angels scored in each of the first three innings. Juan Rivera hit a two-run single in the first and Morales led off the second with his 10th homer.
Kevin Kouzmanoff drove Saunders' first pitch of the sixth into the left-field bullpen for his seventh home run, the 12th straight interleague game in which he's had a hit. He also homered in Friday's series opener.
Mathis chased Geer with a homer into the lower seats in the left-field corner after a two-out double by Maicer Izturis. The homer was the first for Angels' catcher since Aug. 6, 2006, when he hit a solo shot against Baltimore's Garrett Olson in a 9-4 win at Angel Stadium.
Thatcher was recalled from Triple-A Portland to replace Peavy on the roster and he plunked his first batter, Erick Aybar, after Mathis' home run.
NOTES: Troy Glaus was the last Angels player to hit three home runs in a home game, doing it Sept. 15, 2002, against Texas. ... Morales has homered in consecutive games for the second time in his career. He also did it Sept. 18-19, going back-to-back on the front end with Mike Napoli each time. ... INF Sean Rodriguez was recalled by the Angels from Triple-A Salt Lake to fill the roster spot vacated when 2B Howie Kendrick was optioned to Salt Lake after Friday night's 11-6 victory.