The Rayos lifted the trophy – their fourth cup title and their first since the 1994-95 season – in front of their home fans in a packed Estadio Victoria.
The hard-fought game remained goalless until the 86th minute, when the unfortunate Santiago García saw his wayward attempted clearance end up in the back of his own net, giving Necaxa the 1-0 lead.
The Diablos Rojos had previously had the ball in the back of the net in the 73rd minute, but the would-be goal was disallowed for offside.
After the own-goal, there was little time for Toluca to attempt to tie the game, particularly after Pablo César Barrientos was sent off in stoppage time with a straight red card.
With the 1-0 victory, Necaxa are the Clausura 2018 Copa MX champions.