Otamendi is the only healthy natural centre-back in the squad meaning Fernandinho, a regular midfielder, started in Wednesday's 3-0 win over Shakhtar Donetsk.
But Guardiola says because of their age he will have to call upon Kyle Walker and Rodri to play minutes at centre-back.
"I didn't have doubts [Fernandinho] could do it," Guardiola said after City's win on Wednesday. "Nico is 31, Fernandinho is 34 and the next alternative (Eric Garcia) is 18. For three or four months I don't know what will happen.
"Both were incredible tonight. Nico showed incredible personality after what happened in the previous game.
"We need another solution -- Rodri or Kyle Walker maybe -- because they cannot play every game at their age."
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