The visitors, already without six first-team players for the game, lost defender Manuel Akanji with a calf issue in the warm up.
Forward Savinho was then taken off on a stretcher in the 63rd minute of the game after appearing to hurt his ankle.
Guardiola also said defender Ruben Dias, who went off at half-time, is “struggling” sometimes.
“We have 13 players, we are in real difficulties,” Guardiola said.
“The guys that play, they finish most of them with problems and we’ll see how they recover.
“I think we are in trouble, because in nine years we’ve never been in the situation with so many injuries.
“The players make a step forward, more together than ever, and we will try to do this week in this short time of recovery.”
Defensive midfielder Rodri is out for the rest of the season after rupturing his anterior cruciate ligament in September.
Attacking midfielder Oscar Bobb is also out long term after fracturing his leg in August. Guardiola said at the time he would be out for “three or four months”., external
Kevin de Bruyne, who missed five months of last season following surgery, is out with a thigh injury and while he was initially expected to be only out short term, Guardiola said recently that he “didn’t know”, external when he would be fit.
Full-back Kyle Walker is out with a knee injury with no date on a potential return, while forwards Jeremy Doku and Jack Grealish have missed recent games with injuries.
Guardiola said he did not expect, external Doku to be fit before the November international break.
Prior to Wednesday’s game, Guardiola had named only seven substitutes against Southampton at the weekend and against Sparta Prague last week, with two goalkeepers included on the bench for the latter.
“Tomorrow we have two goalkeepers and Erling Haaland in the training session,” Guardiola said after the Tottenham loss.
“The rest, we don’t have anything else.”
Going by the squad list on Manchester City’s official website, it does appear that Guardiola’s claim is accurate.
Obviously he will be able to call upon youth-team players, but excluding those injured, these are Manchester City’s available first-team outfield players:
Defenders, Nathan Ake, Ruben Dias, Josko Gvardiol, Rico Lewis, John Stones, Josh Wilson-Esbrand
Midfielders, Phil Foden, Ilkay Gundogan, Mateo Kovacic, James McAtee, Matheus Nunes, Bernardo Silva
Forwards, Erling Haaland
That adds up to 13 outfield players but includes Josh Wilson-Esbrand, who has not made a first-team appearance for the club.
Guardiola said in the build up to Wednesday’s game his main hope was to get through it without any more injuries.
Although they lost to Spurs, the young players in the Manchester City side showed promise and only a brilliant block on the line denied 19-year-old Nico O’Reilly scoring a late equaliser.
Manchester City are top of the Premier League, unbeaten in Europe but have failed to reach the League Cup quarter-finals, and Guardiola said recently if injured players don’t come back soon then his side will struggle to compete in multiple competitions.
“If these guys don’t come back as quickly as possible, we’ll struggle, because we cannot sustain with just 14, 15 players for the season,” he said.
“We need the players to come back.”
