Nova scattered three hits, striking out 11 and walking one, but looked set to take a tough-lock loss with the Orioles leading 2-1 thanks to Matt Wieters' two-run homer in the second.
Travis Hafner drew a bases-loaded walk to tie things up in the bottom of the ninth, though, and Wells' hit gave the Yankees the walk-off win, condemning Orioles closer Jim Johnson to his sixth blown save of the season.
Francisco Liriano also tossed a complete game to fire the Pittsburgh Pirates to a 6-2 win over the Chicago Cubs.
Liriano allowed four hits and four walks, punching out seven, while Starling Marte scored twice on three hits, also stealing two bases.
Tyler Skaggs kept the Colorado Rockies quiet for eight innings to lead the Arizona Diamondbacks to a 5-0 win.
Skaggs allowed just three hits and a walk, fanning five, while Aaron Hill and Paul Goldschmidt each knocked in a pair.
Rick Porcello hurled seven shut-out frames to lift the Detroit Tigers to a 7-0 win over the Cleveland Indians.
Porcello allowed five hits and a walk, striking out six, and got support from Victor Martinez who drove in a pair on three hits.
Mark Buehrle also threw seven scoreless innings, helping the Toronto Blue Jays to a 4-0 win over the Minnesota Twins.
Jose Bautista hit his 20th homer of the season while Jose Reyes drove in a pair on three hits.
Tommy Milone took a shut-out into the ninth as the Oakland Athletics beat the Kansas City Royals 6-3.
Milone ended up allowing three runs in 8 1/3 innings, but Grant Balfour nailed down his 40th straight save to complete the victory.
David Ortiz cracked a two-run pinch-hit homer to help the Boston Red Sox beat the Los Angeles Angels 6-2.
Nelson Cruz launched a grand slam to lift the Texas Rangers to a 10-5 win over the Houston Astros, while Kirk Nieuwenhuis had a career-high five RBIs on four hits as the New York Mets beat the Milwaukee Brewers 12-5.
The Philadelphia Phillies held on for a 5-4 win over the Atlanta Braves, the Washington Nationals beat the San Diego Padres 8-5 and the Tampa Bay Rays overcame the Chicago White Sox 8-3.
The St Louis Cardinals saw off the Miami Marlins 4-1, the Seattle Mariners were 4-2 winners over the Cincinnati Reds and the Los Angeles Dodgers cruised past the San Francisco Giants 10-2.