Ex-Benfica midfielder Sanches returned to haunt his former club, the 21-year-old Portugal international on target as Bayern claimed a 2-0 victory away from home on Wednesday.
Sanches endured a forgettable loan spell at Swansea City last season but he was handed his first Bayern start since May 2017 and repaid the faith, converting James Rodriguez's cross nine minutes into the second half, having played a role in Robert Lewandowski's opener.
Benfica also applauded Sanches – who left the Portuguese giants in 2016 after emerging through the youth ranks – following his display in the Group E clash at Estadio da Luz.
"I'm happy," Kovac said during his post-match news conference. "Like I said in Munich, Renato wasn't going to be our travel guide.
"Actually Thiago [Alcantara] should have played, but when we knew he was going to miss the game, I thought it was the right time to let Renato play.
"What he did tonight was special. You could see why he is such a good player in his young age. A player with high technical and physical skills. And then he even scored.
"I have to make a compliment to him and the Portuguese supporters, that they gave him applause. You don't see that very often. That speaks for their favour."
On the match itself, Kovac said: "We wanted to have a good start in both the Bundesliga and the Champions League.
"We knew Benfica have an exceedingly good team. They have a straightforward approach and try to finish quickly. We had to fight, we had many presentable chances but failed to make the most of them, we could have closed it out earlier.
"We want to go far in the Champions League. We have to stay focused, we know we're being hunted by everyone."
Bayern defender Mats Hummels also saluted Benfica's supporters for their treatment of Sanches post-game, tweeting: "Love it when a stadium does that. Massive respect @SLBenfica fans."
Meanwhile, Benfica head coach Rui Vitoria told reporters: "We wanted to win but faced one of the strongest teams in Europe."