With previous leaders Melgar going down 2-0 at Inti Gas, Alianza pounced in the Peruvian capital, winning their first Clasico since March 2013 to take the lead in Peru's top division.
In a feisty match where both teams finished with nine players, Alianza triumphed thanks to Victor Cedron's goal in the 64th minute, with the substitute finishing from an angle after bursting onto Christian Cueva's through-ball.
Cedron's strike came after both sides had had a player sent off in the 51st minute with Josimar Atoche red-carded for Alianza, while Antonio Gonzales was also dismissed.
In second-half stoppage time, the home side's Roberto Guizasola and Universitario's Rafael Guarderas also received red cards.
The win took Alianza to 18 points, two ahead of Melgar, who suffered just their second defeat this season, while Sporting Cristal moved up to third (14) thanks to Renzo Revoredo's 96th-minute strike, which secured a 3-2 win at San Simon.
Cristal have not lost in five matches.
Union Comercio and Universitario (both 13) sit fourth and fifth respectively, with the former losing 2-1 at Universidad San Simon.
In other games on Wednesday, Real Garcilaso continued their resurgence with a 3-0 thumping of UTC Cajamarca, while Cesar Vallejo overcame Cienciano 3-2 and Leon de Huanuco won 1-0 against Sport Huancayo.
Juan Aurich and Los Caimanes completed a scoreless draw on Tuesday.
