Bartley initially joined Orient on a month's loan at the start of August after struggling with a hamstring injury during pre-season.
He has made four appearances to date for the League One club and started for the first time against Hull City in the Capital One Cup in midweek.
The 24-year-old will now stay until the New Year and Orient manager Russell Slade is expecting Bartley to make an impact.
"We are delighted to keep Marvin on board, particularly as at one stage it looked like we might be losing him," Slade told the club's official website.
"He had a difficult start with us as he wasn't fully fit due to the injury he picked up at Burnley in pre-season.
"However, in training and during the limited minutes that he's had on the pitch, he's shown himself to be a very capable player. Trust me, there's a lot more to come."