The Scotland international has managed just 14 games for club and country in the past year as he fought back from shoulder and hip injuries.
But the 24-year-old was dealt a fresh blow just 10 minutes from the end of the Dark Blues' final RBS 6 Nations clash with Ireland when he damaged his left shoulder once more.
Scott went under the knife last week but he has now been told he will have to be operated on again.
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He will now play no further part this season as his misses out on the Guinness Pro12 run-in and Friday's European Challenge Cup semi-final with Newport Gwent Dragons at Murrayfield.
Confirming the news, an Edinburgh spokeswoman said: " Following an injury to his left shoulder, sustained during the final game of the RBS 6 Nations, centre Matt Scott underwent surgery last week.
"It had been hoped that Matt would be able to manage his injury conservatively but following consultation with specialists at Spire Murrayfield the decision to perform an investigative arthroscopy was taken. This resulted in him requiring a further surgical procedure to help deal with his shoulder complaints.
"Matt will now continue with his rehabilitation programme with the Edinburgh Rugby medical team and he will be unavailable to play for Edinburgh for the rest of the season.
"Everyone at the club wishes Matt all the best with his recovery."
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