The Atlantas have earned a place in the playoffs with a stunning 1-0 win over the Orlando City SC at Papa John Arena.
It is the first time since 2013 that a team from the same division has earned the trophy and it is the third time in five seasons that the two sides have met at the competition.
Atlantans captain and attacking midfielder Georgios Samaras, who scored in the victory, had already put the hosts in front after only the first 30 minutes.
The visitors had taken the lead through the first goal from a free-kick from midfielder Juan Luis Suarez in the 56th minute, and they levelled in the 90th minute through Victor Mansaray.
With their only goal on goal, the Atlantados will now play in the Europa League next season.
The teams met once before in the MLS regular season, when Orlando City scored a late winner to earn the right to face the hosts at home.
The game was played in a 1,500-capacity stadium, which was closed to the public in both the first leg and the tiebreak.
The home side is still awaiting the result of a medical report, and the match will not be broadcast on television.