Nava, a switch-hitter best known for hitting a grand slam on the first major league pitch he saw on June 12, batted for Eric Patterson when lefty Will Ohman replaced Brad Bergesen (3-5) with two outs and Marco Scutaro on second with a double.
Nava popped a 2-1 pitch down the line. First baseman Ty Wigginton, second baseman Julio Lugo and right fielder Nick Markakis gave chase, but the ball dropped in front of Markakis as Scutaro scored easily. Tim Wakefield (3-6) got the win.
J.D. Drew hit two solo homers for the Red Sox. But Nava's hit decided Boston's shortest game of the season, 2 hours, 7 minutes. The previous shortest games lasted 2:32 on May 12 and 20.
Wakefield allowed two runs and seven hits in eight innings for his second win in his last six decisions. But he broke a tie with Roger Clemens for most starts at Fenway Park with 201.
Jonathan Papelbon had two strikeouts in a perfect ninth inning for his 19th save in 22 opportunities.
Before the game, the Red Sox placed catcher Jason Varitek and reliever Manny Delcarmen on the disabled list. There are 10 Red Sox on it, including Josh Beckett, Dustin Pedroia and Victor Martinez.
The Orioles lost for the third time in eight games but scored three runs or less for the 45th time in their 79 games.
Drew's first homer gave Boston a 1-0 lead in the second before Baltimore tied it in the fourth on Markakis' fourth homer. The Orioles took a 2-1 lead in the fifth when Josh Bell singled, took second on a single by Cesar Izturis and scored on a single by Corey Patterson.
But Drew tied the game with his 10th homer when he hit Bergesen's first pitch of the fifth inning into the left field seats.
Bergesen pitched one of his best games of the season but remained winless since May 12.
Notes: The Red Sox called up RHP Robert Manuel and IF Niuman Romero from Triple-A Pawtucket. … Brothers Corey and Eric Patterson played in the same game for the first time since May 25 when Eric was with Oakland. Corey played center field for Baltimore and Eric was in left for Boston. … The Red Sox are 16-2 in their last 17 home games against Baltimore. … Scutaro extended his hitting streak to eight games. … Matt Weiters' eight-game hit streak ended for Baltimore.