The Mexico international, who joined the East London outfit from Bayer Leverkusen for a £16m fee in the summer, was hauled off in the 68th minute of the Premier League game.
Plenty of fans aired their disapproval when the former Manchester United forward walked to the bench, but Bilic's decision proved to be a positive one as Hernandez's replacement Andre Ayew scored in a 2-0 victory over the Terriers.
Hernandez has played in all four of West Ham's league fixtures this season and has scored two goals, both of which came in the club's 3-2 defeat to Southampton last month.
According to BBC Sport, when asked after the win why he brought off the forward, Bilic said: "You have to take a risk, Javier Hernandez was doing everything but we had good players on the bench.
"I noticed a little bit that Hernandez was getting a little tired with those longer runnings and it was the perfect time for Andre to come on. It was not because Javier did not have a good game it was a time to get fresh legs on the pitch."
The result was West Ham's first win of the season, which has moved them up from the bottom of the league table to 18th.