Uefa says its disciplinary panel will judge the case next Wednesday.
The Scots cited a sickness bug affecting nine players and eight members of the backroom staff as the reason for not playing against Serbia on Monday in Albania in a match that would decide the Group 4 winner,
Serbian media reportedly claimed that Scotland players were affected by drinking to celebrate their win against Albania, whom the Scots beat 11-0 five days earlier.
Competition rules say a team refusing to play “loses all rights to payments from Uefa”.
Uefa could award Serbia a 3-0 win by forfeit.
The SFA is hoping for understanding when its case is heard next week and issued a statement on Wednesday confirming the Under-19s could not play the game because of an “outbreak of acute gastroenteritis”.
The statement added: “This 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. A visit was made by a local doctor near the match venue in Durres and upon submitting his findings, the game was postponed.
“We apologised for the unforeseen circumstance to our hosts in Albania and also to our opponents, Serbia. Given the exceptional situation, we emphasised our wish that the match be rescheduled and we have reiterated that stance to Uefa and their match operations department.”
Coach Gareth Evans, whose team also thrashed Cyprus 8-0, revealed that some of the players’ families had also been taken ill.
The former Hibernian player said: “Firstly, the health and well-being of the girls is the most important thing and while they are disappointed not to have been able to play the game after two victories, I was more concerned with making sure they got treated and made it home safely.
“I contacted every one of the girls’ families personally to update them and allay any fears. Some of the players’ families travelled to watch the games and, even though they weren’t staying in the same complex, they took ill as well.
“Our goalkeeping coach [Kevin Stewart] travelled back to Aberdeen via Heathrow, took ill at the concourse in London and had to be treated on the spot.
“I have never experienced anything like it but the main thing is that we are back recuperating and awaiting Uefa’s verdict.
“We remain hopeful they will look sympathetically at the exceptional circumstances.”