Uncapped 22-year-old James Taylor will take his place in the squad for the match, which gets underway at Headingley on Thursday.
Bopara struggled in last week's innings defeat at the Oval as he was carelessly dismissed for nought in the first innings and 22 in the second.
However, the England and Wales Cricket Board insisted his absence from the squad was for personal reasons.
"James has been part of the England Performance Programme for a number of years and has performed consistently for England Lions and now has an opportunity to step up and experience the Test environment," said National selector Geoff Miller.
Taylor, who played in a one-day international against Ireland last year, is included alongside Graham Onions, who missed the first game through injury, and Steven Finn - who was left out the final XI that lost by an innings at the Oval.
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