The devastating finisher had been due to make his club comeback in the fixture but the South African has been sidelined by a wrenched hamstring, sustained during the Springboks' defeat by the All Blacks in Johannesburg at the weekend.
Confirmation of Habana's absence came as the Toulon coach Bernard Laporte dismissed the idea that the Warriors will present an easy first step in his side's defence of the title.
The former France coach said: "Some people think we have a straightforward passage into the quarter finals and that winning our group will be a formality. That is nonsense.
"Glasgow went close to winning the Pro12 title last season and are now top in what is a very hard competition. We also have to play Cardiff Blues, who have many of the players who won the Six Nations for Wales, and Exeter Chiefs, who impress me. "As holders, the pressure will be on us because even more will be expected of us."
Laporte joked: "The trophy has told me it loves the weather in Toulon and it doesn't want to leave because the girls here are so beautiful! That is what I will tell my players before they go out to face Glasgow."
Meanwhile, the Munster captain Peter O'Mahoney is likely to be fit for their encounter with Edinburgh at Murrayfield on Saturday.
The breakaway forward was forced off with a head knock during the Pro12 victory over Leinster at Thomond Park at the weekend.