The 30-year-old paceman failed to take a wicket in England's ten wicket defeat in the first Test in Dubai last week before a back injury returned, leaving him unable to bowl in practice sessions.
Tremlett, who has taken 49 wickets in 11 Tests, missed five months of international cricket after injuring his back last summer.
The fast bowler, who stands at six feet and eight inches, becomes the second casualty for England after paceman Tim Bresnan was forced to return home three days into the tour, failing to recover from elbow surgery undertaken last year.
"Tremlett has been ruled out of the series after a recurrence of a back injury and a replacement will be announced in due course," the England and Wales Cricket Board said.
Left-arm spinner Monty Panesar replaced Tremlett in England's squad for the second Test. England trail Pakistan 1-0 after losing the first Test in Dubai by ten wickets.
The three-Test series will be followed by four one-day and three Twenty20 internationals.
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