Despite being named in the Lions' 22 on Thursday night, coach Michael Voss confirmed on Friday that Hooper would be replaced by veteran Tim Notting on the bench.
The livewire has kicked six goals in the first two games but has failed to come up from an ankle problem and is expected to miss just one week.
Speaking ahead of the Swans clash at the Gabba with vice captain Simon Black by his side, Voss also said nothing should be read into Jamie Charman's omission from the team.
Voss said his most experienced ruckman had rushed his preparation for the good of the team but now needed more game time in the reserves.
''Jamie did us a favour by really pushing himself to get right for round one and we didn't really have any ruck stocks at that particular time,'' Voss said.
''We need Jamie Charman fit and firing because he adds a lot to the group.
''We've got (Matthew) Leuenberger, the emerging one, and Charman, the experienced one. If we can maintain that then that's what we'd like to see. We don't see long-term Mitch (Clark) playing that (back-up) role.
''We just thought Jamie needed some more game time in his preparation. He battled manfully at the end of last year and I just don't want to see him do the same for the rest of the year.
''(He needs to) get himself right so he's feeling comfortable and confident.''
Without a win against the Swans since round one 2004, Voss said the Lions were now following the work ethic created by the Sydneysiders as the model for success.
''The way they go about their footy and they way they're regarded as a footy team has been long admired so obviously as a group if we could build towards something like that we'd be very pleased,'' he said.
''You've got to compete to the end to beat them. They force you to be able to beat them in the contests and they really challenge the opposition.
''You don't ever feel like you've got a safe lead against them because they've got that character to build momentum across a game.''
Black was in total agreement with his coach, saying the Swans had been the benchmark for the last few years.
After missing round one against the West Coast with the flu, Black returned strongly against Carlton last week and said he was keen to get amongst the tough stuff against the Swans tomorrow night.
''You know it's going to be a four-quarter game and you've just got to keep at it, keep at it, contest to contest; they like one on one footy and you've got to do it too,'' he said.
''It's hard work – it's a real scrap, stoppage after stoppage.''
