John Stones lasted just 45 minutes on his return to the Manchester City starting XI after suffering a recurrence of an earlier injury.
The defender was included in the squad for the first time since late last month after the champions suffered a 2-1 defeat to Aston Villa.
Stones, who has been plagued by a string of problems over the past two seasons, came on for Ruben Dias, who suffered an injury against Manchester United that is expected to keep him out for four weeks.
Following City's loss to Unai Emery's side – their ninth in 12 games – Guardiola revealed the half-time substitution was forced after the England international suffered a setback.
The 30-year-old has made just one 90-minute appearance in the Premier League this season, having been limited to just 16 appearances last season.
By the time the former Everton star left the pitch on Saturday afternoon, his side were already behind, thanks to John Duran's fifth goal in as many starts.
Stones was replaced by his England team-mate Kyle Walker after the break, but the champions' fortunes did not improve as Morgan Rogers doubled their lead late in the match.
A rare and very minimal ray of sunshine brought consolation to City's goalscorer. Phil Foden found the back of the net in stoppage time to end his goal drought in the top flight.
The result puts City in sixth place and nine points ahead of leaders Liverpool, having played two more games than Arne Slot's men.
'[The end of this run] It may come, it may not come,” Guardiola said. 'It depends on us, the opponents and the results. The solution is to bring the players back.
'We have one fit central defender and that makes it more difficult. We'll try it in our next game. It's another opportunity – don't think much beyond that, recover well and try to do it.'
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