In the top of the fifth, with the American League trailing 1-0, Suzuki hit a two-run, inside-the-park home run off Young to give the AL a lead they never relinquished en route to a 10th straight victory around the 2002 tie in Milwaukee.
Baltimore second baseman Brian Roberts drew a lead-off walk from Young, who was one of three Padres pitchers used by the National League.
After Young retired Yankees catcher Jorge Posada on a fly to center, Suzuki drove a line drive off the wall in right. As the NL outfielders ran down the ball, the swift Mariners outfielder never slowed in his race around the bases to get the first inside-the-park home run in All-Star Game history.
Young would retire the next two hitters in the inning. But the damage had been done. The AL led 2-1. They would hold leads of 3-1, 3-2 and 5-2 before the NL scored two runs in the bottom of the ninth. Angels closer Francisco Rodriguez would then retire Philladelphia center fielder Aaron Rowand on a bases-loaded fly to right to end the game.
Suzuki's drive earned him the game's Most Valuable Player award. The center fielder was 3-for-3.
Padres right-hander Jake Peavy followed Randy Jones (1976) and LaMarr Hoyt (1985) to become the third Padres pitcher named the NL starter in the All-Star Game. Peavy, who would win the NL Cy Young Award in 2007, allowed a game-opening single to Suzuki in a scoreless inning - as the NL had nine pitchers work one inning apiece.
Padres reliever Trevor Hoffman allowed a hit in a scoreless ninth.
The NL took a 1-0 lead in the bottom of the first when Mets shortstop Jose Reyes opened the game with a single off AL starter Dan Haren of the Oakland A's. Reyes stole second and scored on a two-out single by Cincinnati right fielder Ken Griffey Jr.
Suzuki's homer put the AL on top and the lead was upped to 3-1 in the top of the sixth when Tampa Bay left fielder Carl Crawford homered off Milwaukee's Francisco Cordero.
Mets center fielder Carlos Beltran opened the bottom of the sixth with a triple off Detroit's Justin Verlander and scored on Griffey's sacrifice fly.
The AL made it 5-2 in the top of the eighth. After giving up a single to Boston third baseman Mike Lowell to open the inning, Mets reliever Billy Wagner retired the next two AL hitters. Cleveland catcher Victor Martinez then hit a two-run homer.
Mariners reliever J.J. Putz retired the first two NL hitters he faced in the ninth before the senior circuit rallied and almost pulled the game out.
The two-out rally started when Washington's Dmitri Young, who was pinch-hitting for Hoffman, singled. Cubs left fielder Alfonso Soriano cut the deficit to 5-4 with a two-run homer.
Still, the AL needed only one more out. After Putz walked Milwaukee shortstop J.J. Hardy, he was replaced by Rodriguez, who issued back-to-back walks to Cubs first baseman Derek Lee and Arizona second baseman Orlando Hudson to load the bases.
Rodriguez then got Rowand to fly out to end the game and earn the save.
Haren and Boston's Josh Beckett each worked two innings for the AL at the start of the game with Beckett getting credit for the win. Young was tagged with the loss.
Suzuki had three of the AL's 10 hits. No one else had more than one. Reyes was 3-for-4 with a double and a steal as the lone NL player with two hits.
The third All-Star Game played in San Francisco was the first played at AT&T Park.