While Carlos Lobaton's penalty just after the hou- mark saw Sporting Cristal triumph on Wednesday in Lima, the Peruvian hosts missed a multitude of chances to further extend their lead ahead of next week's second leg in Brazil.
Sporting finished the game with five shots on target and 12 corners, compared to four and four for Atletico PR.
The home side took the lead in the 30th minute when Irven Avila collected Leandro Leguizamon's header into the left channel, burst away from Atletico PR's defence and finished through the legs of visiting goalkeeper Weverton.
Atletico PR equalised 10 minutes into the second half thanks to Ederson's well-placed spot-kick after Horacio Calcaterra had fouled Natanael Pimienta in the box.
Sporting went ahead again only six minutes later with captain Lobaton recovering from Manoel's illegal challenge to slot his penalty into the top corner.
But the hosts were unable to score again after the spot-kick, despite getting free in behind Atletico PR's defence several times.
Atletico PR will host the second leg on February 5 with a spot in the group stage of the Copa Libertadores on the line.
In the other match on Wednesday, Deportivo Quito won 1-0 at home against Botafogo.
The Ecuadorians took the lead in the 19th minute at the Estadio Olimpico Atahualpa in Quito when Victor Estupinan converted from inside the penalty area following an initial save from Botafogo goalkeeper Jefferson.
