Quintero made his first appearance of the 2012–13 CONCACAF Champions League on 21 August 2012, scoring a hat-trick in a 5–0 victory over C.D. Águila in the first match of the group stage. In their next match, he would find the back of the net again to help Santos to a 3–1 victory over Toronto FC. After losing the first leg of the quarterfinals away to the Houston Dynamo 1–0, Santos responded with a 3–0 win in leg two to advance to the semifinals. Santos won the first leg with the Seattle Sounders 1–0. In the return leg Santos managed a 1–1 with Quintero scoring to help send "Los Guerreros" to their second consecutive CCL final, facing Monterrey once again. After a scoreless first leg, Quintero opened the scoring in leg two with a goal in the 38th minute. With Santos up 2–1 late, Quintero was subbed off in the 82nd minute. Soon after Monterrey would level the score at 2 in the 83rd minute, before taking the lead in the 86th. Rayados would add on another goal in stoppage time to defeat Santos 4–2, defeating Santos in consecutive CCL finals and taking their third consecutive Champions league title. Quintero's 6 goals in the tournament saw him tie for the golden boot with Nicolas Muñoz.