Dzeko was crowned the winner following his performance in as Roma beat CSKA Moscow 3-0 , contributing two goals at the Stadio Olimpico in Rome.
The 31-year-old beat other nominees Mohamed Salah who scored two goals as the Premier League side beat Crvena Zvezda 4-0.
other nominees for the award include David Silva who played a huge role as reigning Premier League champions Manchester City beat Shakhtar Donetsk 3-0 away from home.
While Borussia Dortmund's defender Achraf Hakimi was also on target as they won 4-0 against Atletico Madrid.
Dzeko finally emerged winner as he lost out to Lionel Messi.
Champions League Team of the Week
For his performance against CSKA Moscow, Dzeko was included in the Champions League Team of the Week.
Dzeko leads the attack in the Team of the Week and is joined by two of the nominees for the Player of the Week award.
Angel Di Maria wins Goal of the Week award
Paris Saint-Germain midfielder Angel Di Maria has emerged as the winner of the Goal of the Week for Matchday three.
The 30-year-old beat other nominees Lorenzo Insigne's opener for Napoli against PSG, Marcelo's goal for Real Madrid against Viktoria Plzen.
With the final nominee Manchester City's Bernando Silva for his solo strike against Shakhtar Donetsk.
Ruben Loftus-Cheek wins Europa League Player of the Week
Chelsea is the winner of the UEFA Europa League Player of the Week award for matchday three.
He was given the award after he scored a hat-trick at Stamford Bridge as Chelsea beat BATE Borisov.
Europa League Team of the Week
Ruben Loftus Cheek also took a place in midfield in the Europa League Team of the Week for matchday three.