Madrid pushed for a winner throughout the second half, and Vinicius eventually found the net in the 87th minute with a viciously struck long-range shot.
Sevilla started well and didn't take long to go ahead as Mir was allowed space and time to guide a free header past Thibaut Courtois.
With Madrid reeling, the forward followed up with two chances in quick succession as David Alaba cleared a shot off the line before Mir was denied again seconds later by Courtois.
Lucas Ocampos hit the crossbar with a curling shot before Madrid levelled. Benzema reacted quickest when Militao's speculative effort from distance was fumbled onto the post by Bono.
Referee Jose Sanchez Martinez waved away Sevilla's penalty appeals when Ocampos appeared to be fouled by Alaba, and Marco Asensio fired over the bar before half time. Much of the second half proved frustrating for Madrid, as poor decision-making saw them spurn some promising goalscoring opportunities.
Asensio opted to shoot from distance when he had Benzema alongside him in space, before Vinicius blasted off target rather than passing to the France international.
Alaba volleyed over the crossbar before Vinicius' late goal-of-the-season contender, while Courtois saved Madrid with a point-blank stop in added time.