The 5-0 first-leg advantage will ease Bayern's worries over injuries which have ruled out Arjen Robben with a pinched nerve, adding to a list of longer-term absentees including striker Kingsley Coman, 'keeper Manuel Neuer and midfielder Corentin Tolisso.
Thiago is set to sit out Sunday's league match at RB Leipzig with Bayern starting the weekend 20 points clear in a the table.
"However, we need to first focus on the target ahead of us", he said.
Bayern hope a scan on Thiago's foot will not mean another lengthy lay-off after he missed 13 games up until mid-February with a leg injury.
The Bundesliga champions went 2-0 up seconds after the second-half restart when Gokhan Gonul volleyed a Rafinha cross into his own net.
In the 59th minute, Besiktas pulled a goal back thanks to a Vagner Love strike which proved to be a consolation goal.
The draw for the last eight of the Champions League will take place on Friday, with Bayern to be paired with Liverpool, Manchester City, Juventus, Roma, Barcelona, Real Madrid or Sevilla. It means they join Robert Lewandowski, Sebastian Rudy and Joshua Kimmich, as the six Bayern players who are all just one more yellow card away from suspension.
"We lost the ball a lot, especially in the second half and we didn't have the structure in our game that we had wanted".
"Even though the first match was 5-0, it was not easy".
"It is always a special atmosphere to play here, there are few other stadiums like it".
Heynckes was appointed by Bayern for his fourth spell in October following the sacking of Carlo Ancelotti, the Bundesliga side winning each of his European games in charge since then.
Assassination of Rights Defender, Driver
As Franco was leaving the site, a auto pulled up to the side of her own vehicle and fired nine shots into it. Investigators reportedly suspect that Franco, 38, was the victim of a targeted assassination.