Omeruo limped out of the pitch three minutes after the break and was replaced by Roberto Rosales.
Jose Arnaiz netted the winning goal for the home team in the 49th minute.
The 27-year-old has made seven league appearances for Leganes this season.
Nigeria head coach Gernot Rohr will be eager to know the extent of Omeruo’s injury ahead of his side’s 2022 Africa Cup of Nations qualifying double-header against the Leone Stars of Sierra Leone.
Rohr could be without Nantes of France winger Moses Simon for the game.
Simon sustained an injury in Nantes’ 3-0 home defeat against Paris- Saint Germain on Saturday.
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