The stand-in skipper wasn't in the squad for the 1-0 win over City, with Carlos Cuellar taking the armband in his absence.
O'Neill revealed after the game that O'Shea hadn't been feeling 100% for a couple of days, adding:
"We did some training last night and he wasn't really up to it. He hadn't improved today so we left him out.
"It wasn't worth the risk; I hope he'll get over it pretty quickly."