Omeruo was in action as Leganes piked up another three points in front of their home supporters at the Estadio Municipal de Butarque.
The 24-year-old Nigerian centre back was not named in the starting line up by Leganes manager Mauricio Pellegrino.
Omeruo however was on the bench and was introduced in the 29th minute of the first half as due to an injury to central defender Unai Bustinza.
Leganes were already one goal up before Omeruo's introduction as Guido Carrillo converted a pass through to him by Michael Santos in the 14th minute to give the home side the lead.
Omeruo put in a disciplined performance alongside fellow defenders Jonathan Silva, Rodrigo Tarin and Dimitrios Siovas to keep a clean sheet in the encounter as the withstood pressure from Rayo Vallecano.
The Nigerian defender showed calm and composure as he was not bullied in his duels against opposing attackers.
Omeruo is among the Super Eagles players called up for 2019 Africa Cup of Nations (AFCON) double header against Libya.
The victory means that Leganes won back to back games at home after they defeated reigning in their last outing in front of their home supporters and will resume action after the international break against Valencia on Saturday, October 20.