Atlanta United's memorable inaugural MLS season came to a bitter end on Thursday after suffering a penalty shoot-out loss at home to Columbus Crew in the play-offs.

Led by former Barcelona and Argentina head coach Gerardo Martino, Atlanta dazzled this season and the high-scoring MLS entertainers were tipped to advance to the Eastern Conference semi-finals.

However, the Crew – subject of relocation drama amid growing reports of a move to Austin, Texas – held Atlanta scoreless after 120 minutes and stunned the fancied hosts 3-1 on penalties in front of 67,221 fans at Mercedes-Benz Stadium. 

Crew goalkeeper Zack Steffen, who enjoyed a stellar 120 minutes with eight saves, came up big in the shoot-out, denying Julian Gressel and Leandro Pirez as Columbus earned a meeting with New York City.

Columbus almost snatched victory in the 118th but Harrison Afful's header was cleared off the line by Atlanta's Michael Parkhurst, much to Brad Guzan's relief.

Houston Dynamo, meanwhile, also advanced to the next round by outlasting Sporting Kansas City 1-0 after extra time.

An additional 30 minutes were needed to find a winner at BBVA Compass Stadium following 120 scoreless minutes in Houston.

And the Dynamo emerged triumphant thanks to Alberth Elis' 94th-minute goal.

Elis – in the squad for Honduras' inter-continental World Cup play-off against Australia – bundled the ball past Sporting KC goalkeeper Andrew Dykstra.

The Dynamo will take on Portland Timbers in the Western Conference semi-finals.