America, who hold a joint record 13 Colombian league titles with Millonarios, were held 1-1 at home in the second leg of the promotion-relegation playoff, having also drawn the first leg 1-1 at La Independencia in Tunja.
Patriotas, who have earned promotion to the first division in their eighth year having been founded in 2003, reached the playoff as second division runners-up while America were one from bottom in the relegation standings.
Forward Jairo Castillo headed America into the lead from Paulo Cesar Arango’s free kick in the 59th minute but Anuar Guerrero equalized in the 64th.
Castillo then missed his penalty in the shootout as America became the second big South American club relegated this year after Argentina’s River Plate with their players and coach Wilson Piedrahita breaking down in tears on the pitch.
Local media reported there was some fighting outside the ground after the match but gave no further details.
America are four times South American Libertadores Cup runners-up, twice losing the final to River in 1986 and 1996.
Once a rich club owing to their connections with the Cali drugs cartel, America have fallen on bad times after being placed on the so-called Clinton List with their assets in the United States frozen and companies ordered not to do business with them.