A brace from Andreas Weimann saw United go 2-0 down to Aston Villa after 50 minutes.
Hernandez was introduced at half time to deadly effect, earning United all three points with a clinical hat-trick.
The Mexican was adamant after the match that while he enjoyed the achievement, helping United win the match was far more important.
He told Sky Sports News: "To be honest it was not in my mind to change the game, I just wanted to help my teammates.
"I just wanted to go what the gaffer told me before the game, run in behind, move defenders and create chances. Of course I'm claiming the hat-trick, I hit the target [with the second].
"The third was a wonderful cross from Robin van Persie and thankfully I made contact and it went in. But it does not matter who scored the goals or who was the man of the match, just that we got the three points."
Hernandez has now come off the bench to score ten times in his Manchester United career.