Domagoj Vida's red card early in the first leg of their last-16 clash allowed Bayern to take complete control in Germany, running out 5-0 winners and all but eliminating Besiktas before the return fixture.
But Gunes wants his team to show that they belong at this level despite the misery of their last match.
"We wanted to qualify or at least experience an exciting tie, but the big difference [in the first tie] did not suit us well," he told a pre-match news conference.
"We will still try to get a result, playing our best game. We know Bayern have come here with the strongest line-up possible and we will try to play with our best side.
"We are bidding farewell for this year, but we want to leave a good impression as we go with the aim of getting here again next year."
Besiktas are currently second in the Turkish Super Lig, a position that would see them enter next season's Champions League at the second qualifying round.