The forward was left out of Nuno Espirito Santo’s side who beat Manchester City 1-0 in their Premier League opener on Sunday amid speculation about his future.
Tanguy Ndombele and Serge Aurier are also not part of the squad that will travel to Portugal.
Kane was the subject of a £ 100million offer from City earlier this summer, which was rejected by Tottenham, and the Premier League champions remain eager to sign the England captain during the transfer window.
The 28-year-old’s omission from Nuno’s squad in his victory over Pep Guardiola’s side has intensified discussions about a potential exit from the club this summer.
Under UEFA rules, if Kane plays for Tottenham in Thursday’s game, he will still be able to play for any Champions League team from the group stage this season.
He took part in Tottenham’s full training last Friday after completing individual sessions during his period of isolation following his late return to pre-season training.
Asked in his post-game interview about Kane’s absence for his first game of the season, Nuno said: “Harry is one of the best players in the world, so we’re very lucky to have him.
“He has to prepare and help the team. We still have to go to Portugal and then we think of Wolves [on Sunday].
“Harry has been working this morning, getting ready and when he’s ready he’ll join the group and help the team.” “
Kane believes he has a gentleman’s agreement with President Daniel Levy to leave his childhood club after reiterating his desire to leave earlier this year, but Levy has hinted that a deal might be difficult to strike, the striker being still under contract until summer 2024..
He was last season’s top scorer in the Premier League with 23 goals, and the Spurs forward has found the net 221 times in 336 games for the club in all competitions.
New rookie Cristian Romero came off the bench in the City win, while Bryan Gil and Pierluigi Gollini were unused substitutes.
Pacos de Ferreira finished fifth in the Portuguese top flight last season and the second leg at Tottenham Hotspur Stadium will be played on August 26.