Xabier Azkargorta's Bolivar earned a 1-1 draw at home to the Liga MX champions in the second leg of their knockout tie.
Tuesday's result was enough to see the Bolivian side through 3-3 on aggregate, after they scored two goals on the road in last week's opening leg.
After shipping two goals at home, Leon knew they had to make a bright start at the Estadio Hernando Siles.
And they did courtesy of Franco Arizala, who opened the scoring inside just five minutes.
Fernando Navarro delivered an-inch perfect cross and the Colombian attacker was on hand to head home for his third goal of the tournament.
Falling behind seemed to spur the home side into life, with Leon goalkeeper William Yarbrough finally forced into action on 14 minutes by Juanmi Callejon.
As the half wore on, Bolivar pushed more numbers forward and they were eventually rewarded with a 36th-minute equaliser.
Defender Ronald Eguino was the unlikely hero, guiding his effort past the helpless Yarbrough.
Leon emerged from the break knowing a 1-1 stalemate would not suffice and their woes were compounded 13 minutes from time when captain Rafael Marquez saw red for a foul on Gerardo Yecerotte.
Gustavo Matosas' men continued to search for a match-winner but their numerical disadvantage proved too great of an obstacle during the closing stages.
Bolivar are now on the verge of their first semi-final appearance since 1986.
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