The former Manchester United star was in action for the LaLiga side as they face Valencia in the Copa del Rey quarter-finals on Thursday, and helped seal a 3-1 victory to advance to the last four.
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Iker Munian put Bilbao ahead in the 35th minute, and the away side looked to be heading into half-time 1-0 up.
But then Valencia drew themselves level just before the break, with Oscar de Marcos scoring an own goal.
However, Bilbao took the lead again before the referee blew his whistle, as Nico Williams scored just two minutes later.
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Ex-Red Devil Herrera fell to his knees in celebration and opened his arms, ready for the goalscorer to embrace him.
But rather than join him, Williams ignored Herrera and instead ran past him with the rest of his teammates.
Herrera remained on his knees with a rather shocked facial expression as the other Bilbao stars celebrated.
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Bilbao then went on to score a third goal in the second half, with Mikel Vesga converting a penalty with 15 minutes to go to seal their place in the next round.
And despite being pied after the second goal, Herrera saw the funny side of Williams' reaction after the game.
Posting a picture and video of the incident on his Twitter, Herrera posted two laughing emojis and said: "When you expect Nico Williams to celebrate with you but you get absolutely ignored."
He then added in Basque: "We are in the semi-finals! Congratulations kids!"
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Elsewhere in the Copa del Rey, Real Madrid saw off local rivals Atletico Madrid with a 3-1 win, with Vinicius Jr. scoring after being the target of 'repugnant and inadmissible' incident before the game.