The hosts currently sit in top spot, but with Union only one point adrift in second position, the Argentinian side remain firmly in the picture for a last 16 place.
Match preview
Junior enter the final group game in pole position, although three teams can still progress to the knockout rounds.
The Colombian side began their campaign with a 1-1 draw against Thursday's opponents before consecutive victories followed in matchdays two and three.
Fluminense handed Junior their first defeat of the group stage, but a 2-0 victory over Oriente Petrolero ensured that Thursday's hosts head into the final matchday in top spot.
If Junior collect three points in midweek then they will book their place in the last 16, while a defeat could see them leapfrogged by Union.
A draw, meanwhile, would leave them in a vulnerable position as both Atletico Junior and Union would be overtaken in the standings by Fluminense if the Brazilian outfit manage to beat Oriente.
The visitors, on the other hand, have accumulated nine points from their five group games, leaving them in second place ahead of Thursday's contest.
Despite sitting a point adrift of their opponents, Union are yet to lose the Copa Sudamericana this season, with their five group matches resulting in two wins and three draws.
As well as drawing against Atletico Junior on matchday one, Union's two games against Fluminense both ended in goalless draws, while they managed to beat Oriente on two occasions.
With a win required on Thursday, the visitors will be concerned that their last eight games in all competitions have yielded one victory.
They can at least take inspiration from their solid defensive displays in the group stage, having kept three consecutive clean sheets in the Copa Sudamericana.
Atletico Junior Copa Sudamericana form:
Atletico Junior form (all competitions):
Union Copa Sudamericana form:
Union form (all competitions):
Team News
The hosts will have to cope without Jorge Arias, who will serve a one-match suspension for an accumulation of yellow cards.
With Arias suspended, Alfonso Simarra could come into the starting XI to partner Daniel Rosero in the centre of defence.
Daniel Giraldo was suspended for matchday five, but the midfielder will be included in the lineup for Thursday's contest.
As for the visitors, they have doubts over the availability of Diego Polenta after the defender picked up an injury in Union's goalless draw against Fluminense last week.
If Polenta is not fit enough to feature on Thursday then he could be replaced in the starting lineup by Federico Vera.
With a win required to reach the last 16, Union will be hoping that a front two made up of Mariano Peralta Bauer and Jonatan Alvez can provide a significant goal threat.
Atletico Junior possible starting lineup:
Viera; Viafara, Rosero, Simarra, Fuentes; Moreno, Giraldo; Albornoz, Cabrera, Hinestroza; Borja
Union possible starting lineup:
Mele; Vera, Britez, Calderon, Esquivel; Diale, Roldan, Portillo, Zenon; Peralta Bauer, Alvez