Five top teams from each participating country – Estonia, Latvia, and Lithuania – along with the winner of the 2008 season will play a 4 round and 2 legged (excluding final) play-off style knockout tournament.

The second leg match was scratched and Vėtra advanced to the next round as Dinaburg was ejected from the competition for match-fixing.

Ekranas advanced to the next round 3–2 on aggregate.

Levadia advanced to the next round 3–1 on aggregate.

Skonto advanced to the next round 4–1 on aggregate.