Shakthar progress into the next round of the Europa League having beating Braga 4-2 in their sixth win from sixth.
Braga, however, missed out due to a late Gent goal at Konyaspor, putting the Belgians through with a 1-0 win.
Sergey Krivtstov opened the scoring for the hosts, his header too strong for Marafona in the Braga goal.
Taison then doubled Shakhtar's lead after a stunning solo run from Marlos led to the winger tapping into an open goal.
Nikola Stojiljkovic then pulled one back for the home sides before half time, but Krivstov scored his second of the game with another header.
Taison then made it 4-1 with an impressive run and a poked effort under the goalkeeper before Nikola Vukcevic struck a late consolation.
At the full time whistle Braga stood to qualify, bettering Gent's goal difference, but crashed out when the Belgian side struck a late winner in Turkey.