The Essex batsman ruled himself out of contention for the second Test between England and South Africa at Headingley due to personal reasons but was due to return for the Lions on Tuesday.
Bopara informed the ECB that he would not be playing in the match and has not set a date for a comeback.
The 27-year-old said: "I thought I was ready to return to action - but after some consideration, I just feel it's too early.
"So I won't be playing quite yet."
In the match at Old Trafford, England Lions reached 140-4 at stumps after rain only allowed 66 overs of play on day one.