With heavy rain and a slick field disrupting the rhythm of the game, there were few chances of note in the first half until the end of it.
A shot from outside the box by Alexander Mejía slipped through the hands of Alfredo Talavera to make it 0-1 for León in the 41st minute.
But Toluca responded in the second half. In the 51st minute, Fernando Uribe made it 1-1 with his header before Carlos Esquivel put the Diablos Rojos in front in the 59th minute with his shot from outside the box.
However, that lead lasted for just two minutes before Germán Cano made it 2-2.
But once again Toluca rallied with a pair of goals in quick succession. Erbin Trejo restored the lead in the 65th minute and then Uribe added his second of the night in the 70th to give the hosts a comfortable 4-2 lead.
A headed goal by Mauro Boselli in the 84th minute brought León back to within a goal and ensured a frenetic finish, but in the end Toluca held on for the victory.
With the 4-3 win, Toluca advances to the quarterfinals while León is eliminated.