Having weathered the Besiktas storm, Bayern would get their third on the night and eighth of the tie with six minutes remaining, as unmarked substitute Sandro Wagner chested in David Alaba's deflected cross from three yards out to restore Bayern's two goal lead on the night.
Bayern Munich midfielder Thiago Alcantara is convinced his side can make a serious assault on the Champions League this season.
Despite their massive first-leg lead Bayern made a bright start, Arturo Vidal heading wide.
David Alaba nearly opened the scoring for the Bavarians in the 11th minute with a free-kick that was parried away by Besiktas shot-stopper Tolga Zengin, while Thomas Muller could not turn home the rebound.
Thiago limped off before half-time, giving Bayern an injury concern for the rest of the season.
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Thankfully for Gonul, that remained the most weird moment of the match for only a matter of minutes, before the appearance of a cat on the pitch brought the match to a brief halt.
Bayern Munich have won their last five Champions League games, the longest current run in the competition.
Bayern's coach Jupp Heynckes listens to a reporter's question during a news conference in Istanbul, Tuesday, March 13, 2018, ahead of his team's Champions League round of 16 second leg football match against Besiktas Wednesday.
In the 59th minute, Besiktas pulled a goal back thanks to a Vagner Love strike which proved to be a consolation goal.
RB broke a three-match losing streak in the league when Augustin scored in their 1-1 draw at home to Dortmund a fortnight ago.