Annabel Blanchard and Abbie Larkin had Palace two goals to the good in the first-half before Hughes added a third on the 80 minute mark.
Océane Hurtré got a goal back for the Blues on 89 minutes, but Palace held firm to take all three points back to South London.
Hughes spoke to the media after the game, and had high praise for her teammates.
She said: "I thought the performance from start to finish had a bit of everything.
"I thought in the first half we showed real quality for the goals that we scored and then in the second half we did what we needed to do to secure the three points and I'm really proud of the girls in the changing room.
"In this league you're never going to come up against an easy team and Birmingham definitely aren't that, they're not sitting where they are on the table for no reason, we knew it was going to be tough."
