The 24-year-old rejoined the O's in January until the end of the current campaign.
Former Fulham trainee Omozusi had his contract at Brisbane Road terminated in November 2011 after he was sentenced to two-and-a-half years in prison.
Orient manager Russell Slade told BBC Sport: "I know he's really focused on getting himself back into the side and getting a regular slot.
"There's a really good player in there as we know from two seasons ago.
"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."
Omozusi has made six appearances for Orient this season.