A long clearance from debutant goalkeeper Jonathan Mitchell eluded home defender Shaun Brisley and allowed Marriott to lob keeper Alex Cisak.
Brisley was later stretchered off and hospitalised with a head injury after receiving lengthy treatment when injured colliding with Mitchell.
Dan Potts went close to making it 2-0 after the break, but curled wide.
Leyton Orient manager Kevin Nolan told BBC Radio London:
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"The most disappointing thing for me is that we conceded a very sloppy goal.
"I must admit I was quite disappointed with the referee today but I don't want to go on about that because I'll end up getting in trouble.
"I thought today we were very good, we dominated the game and didn't really give them any chances. I don't think they offered a lot going forward but they defended fantastically well."
Luton boss Nathan Jones told BBC Three Counties Radio:
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"I'm massively proud in terms of what they gave me today, their endeavour, how they went about their work.
"They gave me absolutely everything today and that is all you can ask.
"There was one bit of quality in the game, Jack produced it and it won the game.
"I'm really proud of the players, I'm getting to know what they will produce. There is an equilibrium to their performances and I like that, I can work with that. It's a platform."
Jack Marriott scored the only goal of the game at Leyton Orient to extend Luton's winning run to four games.