After drawing 1-1 in the first leg, Shakhtyour went in front after 17 minutes when midfielder Rodrigues Jadson slotted in from just outside the area.
Ognjen Vukojevic had a goal disallowed as Dynamo fought back and soon after the break they levelled when Guinea striker Ismael Bangoura converted Olexandr Aliyev's fine pass.
With the match seemingly destined for extra-time Ilsinho won it in superb fashion, jinking in from the right and keeping his cool to shoot into the bottom corner.
In the process, Shakhtar became the first Ukraine team to reach the Uefa Cup final.
Shakhtar Donetsk: Pyatov, Srna, Ischenko, Chigrinsky, Rat, Ilsinho (Lewandowski 90), Hubschman, Gai (Willian 70), Fernandinho, Jadson, Luiz Adriano (Gladkyy 70).Subs Not Used: Khudzamov, Duljaj, Seleznyov, Chyzhov.
Booked: Hubschman, Gladkyy.
Goals: Jadson 17, Ilsinho 88.
Subs Not Used: Shovkovskiy, Ghioane, Kravchenko, Nesmachniy, Zozulya, Yarmolenko.
Booked: El Kaddouri, Bangoura, Aliev, Vukojevic.
Goals: Bangoura 47.
Att: 24,000.
Ref: Olegario Benquerenca (Portugal)
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