Juan Reynoso's men defeated Universitario in dramatic fashion, with substitute Bernard Cuesta scoring in the 93rd minute to lift Melgar to a 2-1 victory at the Estadio Nacional de Lima on Wednesday.
The win, coinciding with Inti Gas' 1-1 draw at home to 10-man UTC Cajamarca on the same day, not only extended Melgar's undefeated streak to seven games but saw the club rise to the summit.
Melgar have collected 15 points after seven rounds to be a solitary point clear of Inti Gas and Cesar Vallejo, who accounted for Sport Huancayo 2-0 courtesy of second-half strikes from Luis Tejada and Daniel Chavez.
Table-topping Melgar travelled to Universitario with three wins and three draws from their opening six matches but Christofer Gonzalez's 23rd-minute breakthrough goal threatened to end the club's blemish-free start.
Gonzalez pounced on a failed clearance inside the penalty area to fire the pall past Melgar goalkeeper Leao Butron from the edge of the six-yard box.
Universitario's lead lasted only 20 minutes, however, as Mario Soto levelled proceedings with a thunderous long-range effort.
The visitors completed their comeback in the third minute of injury time - second-half substitute Buesta finding himself in space between two defenders outside the box before lobbing the ball over onrushing keeper Carlos Caceda.
In other results on Wednesday, 10-man Real Garcilaso made it three wins on the bounce after edging Union Comercio 1-0 thanks to Victor Ferreira's 16th-minute opener.
Guillermo Tomasevich scored 11 minutes from time as Leon de Huanuco prevailed 1-0 at home to Alianza Alima.
Goals from Luis Alvarez, Santiago Silva and Jersson Vasquez inspired Universidad San Martin to a 3-1 victory over Los Caimanes on Tuesday.
Elsewhere, two goals in the space of four minutes from Gary Correa saw Cienciano dispose of San Simon 2-0 on Thursday.
A four-goal first half and Carlos Lobaton's brace helped Sporting Cristal to a thrilling 4-3 victory at fifth-placed Juan Aurich.
