The duo have been left out of the travelling squad along with Franck Ribery, but the Frenchman is expected to join the group later after the birth of his child.
Manager Niko Kovac explained ahead of the key clash that centre-back Boateng is out due to illness, while Robben has been struggling with a thigh injury since November:
Kingsley Coman was a doubt after hobbling out of Friday's 3-2 win at Augsburg, in which he scored twice.
He has been given the all clear and included in the squad, but there still seems to be some doubt over whether he will start:
Bayern are back in the Bundesliga title race after winning nine of their last 10 matches, and they pose a big threat to Liverpool's progress in the Champions League.
The Reds made the final last year before losing to Real Madrid.
This season's tournament has already been tough for Jurgen Klopp's side as they scraped out of Group C in second place having finished tied on nine points with Napoli.
As a result they were handed a tough draw against Bayern in the first knockout round and will need to make their home advantage count on Tuesday.
The German champions will be looking to get an away goal on Merseyside as well as restricting Liverpool's impressive front line.
If they can avoid defeat at Anfield as well as getting a goal they will be heavy favourites to advance to the quarter-finals.
Having topped Group E ahead of Ajax, Benfica and AEK Athens, Bayern could hardly have been given a tougher last-16 tie than a meeting with Liverpool.
But they have the quality to restrict the Premier League side even without Boateng in the side.
As one of Europe's biggest clubs Bayern are regularly expected to go deep in the Champions League.
Despite reaching four semi-finals in the last five seasons, though, they have not made a final since they last won the tournament in 2013.
Liverpool pose a major threat to their progress this season, but Bayern will be confident they can get a result at Anfield given their recent form.