The third-tier outfit held firm at their Estadio Provincial Juan Gilberto Funes home, finishing level at 0-0 before winning the penalty shootout 4-1 against Union Santa Fe.
Union Santa Fe, who have performed well in the second tier, were expected to progress but were always in danger once the hosts forced a shootout.
That proved to be the only upset on Wednesday as two other second-tier outfits advanced.
San Martin San Juan managed to get the job done in regulation, claiming a 2-1 home win against third-tier Cipolletti.
Gabriel Chironi put the underdogs ahead on 37 minutes but the hosts levelled early in the second half.
Lucas Salas struck a dramatic late winner just a minute before full-time for San Martin San Juan.
The clash between Patronato and Instituto finished 2-2 before the latter claimed a thrilling 5-4 shootout win.
Instituto had twice come from behind and made the most of doing so by clinching the shootout victory.
'I would love to relive walking out at Wembley in the FA Cup final with West Ham when I was captain': Gilly Flaherty reflects on sensational career
'When Manchester City play it's hard not to be biased as they are my club and I love it when they win - but it frustrates me even more when we get beat' Steph Houghton on the problems of punditry and remaining neutral
