The City midfielder withdrew from the Portugal squad after picking up a knock in their 0-0 draw with Italy on Saturday and will not recover in time to play at the London Stadium.
However, Pep Guardiola says Nicolas Otamendi, who has been missing since the 3-0 win away at Shakhtar in late October, is fit and ready to play.
“Bernardo cannot play this weekend,” Guardiola said.
“The injury is not too big but this game, no, I don’t know if he is available next Tuesday [when City play Lyon away].
“Yeah, [Nico] is back. Everyone else is okay.”
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Benjamin Mendy, Kevin De Bruyne and Claudio Bravo all remain sidelined with long-term problems, but the rest of the squad are fully fit.
Guardiola says Mendy will be out for “10 to 12 weeks”.
Meanwhile, Guardiola has praised former Blues boss Manuel Pellegrini.
The Chilean was in charge at City for three seasons, winning the Premier League and League Cup in 2014, before handing over the reigns to Guardiola in 2016.
Guardiola says Pellegrini has had a fine career and believes he has creates teams that play with a distinct, attractive style.
“His career speaks for itself in terms of the quality," he said.
"When you see the teams of Manuel Pellegrini, when you are blind you recognise his style.
"He put this team on another level. The way they played and created a style was impressive.
"He went to Real Madrid [in 2009] and made 96 points. It was good. Here he won the league and helped this club be where we are right now.
"He will do well at West Ham where there are many good supporters."