They are also angry at reports the players had been too hungover to play.
Uefa has begun disciplinary proceedings and say that the case will be dealt with by its Control, Ethics and Disciplinary Body on 28 September, citing Scotland's "refusal to play".
The SFA says the team suffered from "an outbreak of acute gastroenteritis".
The Scotland women's U19s were due to play Serbia in Albania in the final game of their Uefa European Championship qualifying round robin.
Gareth Evans' side had already defeated Cyprus 8-0 and hosts Albania 11-0, but pulled out of the game with Serbia with nine players from the squad and eight members of the backroom staff ill, calling it an "exceptional situation."
Reports in the Serbian media suggested the players had got drunk the night before and were too hungover to play, something which has angered the SFA.
BBC Scotland also believes the governing body are unhappy with the poor hotel conditions their players were subjected to during their stay, with the walls affected by damp.
"This (the illness) was flagged to Uefa via the match delegate on the day of the match and contact was subsequently made with the Albanian FA to verify the developing illness," the Scottish FA said in a statement.
"A visit was made by a local doctor near the match venue in Durres and upon submitting his findings, the game was postponed."
Head coach Evans also revealed goalkeeping coach Kevin Stewart took ill at Heathrow Airport while travelling back to Aberdeen and had to be treated there.
"I have never experienced anything like it but the main thing is that we are back recuperating and awaiting Uefa's verdict," said Evans.
"We remain hopeful they will look sympathetically at the exceptional circumstances."
The Scottish FA has defended its decision not to field a side in Scotland's Under-19s women's qualifying tie with Serbia on Monday.