The 24-year-old rejoined the O's in January following his release from prison and made six appearances before a shoulder injury ended his season.
However, Omozusi has done enough to impress manager Russell Slade and earn another deal at Brisbane Road.
Slade told the club website: "It was difficult for Elliot over the last few months because he didn't have a pre-season but he's already set his stall out and is doing extra training at Crystal Palace athletics stadium, so he'll be firing on all cylinders for next year.
"I know he's really focused on getting himself back into the side and getting a regular slot and we saw in flashes this year that he's capable of it.
"There's a really good player in there as we know from two seasons ago and I'm really pleased that he's still going to be with us next season."