Alomar had entered the game in the top of the sixth and came to bat with two out in the seventh and Yankees left fielder Bernie Williams on second with two out.
Alomar drove a pitch from Shawn Estes of the San Francisco Giants into the left field seats. The blast earned Alomar the Most Valuable Player award, making him the first player ever to be named the game's MVP in his home ballpark.
Sandy's brother Roberto Alomar of the Baltimore Orioles was the starting second baseman for the AL. Both Alomars started their Major League careers as San Diego Padres.
Pitching and the home run dominated the 68th All-Star Game, which was also the first where AL fans could vote for a designated hitter.
They made a good pick with the selection of Seattle's Edgar Martinez, who homered leading off the bottom of the second against Atlanta's Greg Maddux to give the AL a 1-0 lead.
The National League tied the game in the top of the seventh when Braves catcher Javy Lopez opened the inning with a home run off Jose Rosado of the Kansas City Royals.
That was only one of three hits the NL would get off eight AL pitchers. The AL had seven hits with Martinez and Baltimore outfielder Brady Anderson, a native of San Diego County, having two apiece.
Randy Johnson of the Seattle Mariners started the game for the AL and allowed a walk with two strikeouts in two innings and was involved in an unusual moment. Johnson's first pitch to Colorado's Larry Walker in the second inning sailed far over the left-handed-hitting right fielder's head. Walker backed out of the batter's box, turned his batting helmet around and took a strike from the right-handed batter's box.
Despite giving up the homer to Lopez and two of the NL's three hits, Rosado was the pitcher of record when Alomar homered and was credited with the win. Estes was the losing pitcher.
Yankees closer Marino Rivera struck out one in a perfect ninth to get the save.
Starter Maddux and Schilling of the Phillies each pitched two innings for the NL.
The Padres' Tony Gwynn and Ken Caminiti were both voted into the NL starting lineup. Gwynn was 0-for-3 as the starting NL designated hitter. Caminiti, who had been the unanimous pick as the NL's Most Valuable Player the previous season, started at third and was 0-for-2.
Tino Martinez of the New York Yankees won the Home Run Derby.