The 20-year-old pounced in with one minute of normal time remaining at the New Den, sealing the Lions' place in the fifth round of the FA Cup.
Marquis has struggled with a groin injury this campaign, which has restricted him to just one appearance from the substitutes' bench.
"I'm very happy - it's been a long time since my first start," said Marquis. "To play today, score the winning goal, and get us through to the next round of the FA Cup is a really good feeling.
"I'm not going to rest on my laurels. I want to keep scoring goals and drive the team forward."
Marquis scored one goal in 21 appearances in all competitions last season.