The German club ended Russian outfit Rubin Kazan's run in the competition, winning 2-1 on the night and 3-2 on aggregate.
After the first leg ended 1-1 in Russia, last season's German Bundesliga champions were favoured to get the job done and they did but made very hard work of it.
Rubin's Alan Kasaev gave his side the ascendency in the 21st minute to put his team ahead both on the night and on aggregate.
But in the 58th minute, Obafemi Martins drew the tie completely level with a header which eventually sent the match into extra-time.
In the final minute of the second half, however, Gentner blasted home after god lead-up work by Martins to give his side a last-gasp win and qualification for the final eight.