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."

More than 700,000 private messages between members have also been leaked.
A message on the site's homepage said: "We have been made aware of an alleged security breach and we are reviewing our systems as we work to remedy the situation and tighten our security."
The leaked details included sensitive information such as whether a member would consider polygamy.
The breach was discovered by security researcher Troy Hunt who runs a cybersecurity alert website.
Details of members' employers, location, marriage status and whether they were a convert to Islam were revealed, as well as names, email addresses, Skype handles and IP addresses - according to technology news site Motherboard.
Muslim Match's Facebook page describes the site as: "Single, divorced, widowed, married Muslims coming together to share ideas, thoughts and find a suitable marriage partner."
One of the leaked messages read: "I wanna marry you - if u agree I send my photos and details."
Another read: "You will enjoy when you speak to me, I am genuine and truthful and am seriously seeking a right muslimah who could be a friend, a companion to hold hands thru journey of life and beyond."
The bulk of users affected are believed to live in the United Kingdom, United States and Pakistan.
The website's operation has been temporarily suspended. The company said it will be closed until Ramadan ends this week.

A fault at the Clydesdale Bank machine in Stewarton Street, Wishaw, meant customers received double the amount of money they keyed in.
It is understood about 100 people queued up at the ATM after hearing about the fault at 19:00 on Friday.
A spokeswoman for Clydesdale Bank later said the problem had been corrected quickly.
She said: "We don't operate our ATMs directly as they are outsourced to other suppliers.
"What has happened is that while the machine was being filled, some of the cassettes were placed in the wrong order, meaning that double the amount of money was available."
She added she could not confirm the amount withdrawn, because the bank could not reveal how much was kept in any ATM for security reasons.
In January, dozens of people took advantage of a cash machine in Fintry Road, Dundee, which also paid out double the requested amount.
The machine's operators later said customers would not have to return the extra money.
Jack Marriott scored the only goal of the game at Leyton Orient to extend Luton's winning run to four games.
[NEXT_CONCEPT]
The personal details of more than 150,000 members of dating website Muslim Match have been posted online.
[NEXT_CONCEPT]
Cash machine users doubled their money when an ATM started giving out free cash in North Lanarkshire.