Seijas struck in the 85th minute, poking home a rebound after Nacional goalkeeper Franco Armani thwarted Santa Fe gloveman Camilo Vargas from the spot.
The victory took Santa Fe to 11 points in the Colombian Primera A Clausura semi-final group stage, level with Atletico Huila, although they moved above their rivals due to their superior performance in the regular season.
Santa Fe will face Medellin for the title in a two-legged final, which will begin on Wednesday.
With five minutes remaining in Medellin, Santa Fe looked set to miss out on the Primera A decider as they were locked at 0-0 with Nacional, while Huila led Once Caldas 2-1.
That left Huila on 11 points in Group A's live table, while Santa Fe had just nine.
The visitors were awarded a penalty in the 85th minute, however, and while their goalkeeper failed from the spot, Seijas was the first to respond, sliding in to hook the ball over a diving Armani to clinch victory for Santa Fe.
In the other Group A fixture, Huila defeated Once Caldas 2-1 thanks to goals from John Lozano and Hernan Hechalar in the space of eight second-half minutes.
Lozano struck in the 61st minute before Hechalar doubled Huila's lead in the 69th minute and although Johan Arango hit back for the home side with 14 minutes remaining, the visitors held on to triumph.
In Group B, Medellin topped the standings on 11 points despite a 2-1 loss at Deportivo Cali, who went on to finish second with eight points.
Aguilas Pereira (seven points) beat Deportes Tolima 2-1 to avoid finishing bottom of the group - a dishonour that went to the defeated Tolima (five).
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