Fleck was named in Steve Clarke’s squad for the qualifiers and started in the 4-0 defeat against Russia on Thursday.
It was Fleck’s third senior international call-up after a number of impressive performances for Sheffield United on their return to the Premier League.
However, Fleck’s Scotland debut ended in disappointment with the defeat meaning Clarke’s side will need the play-off they reached by way of the Nations League, if they are to make next summer's tournament.
Scotland recorded their third win in Group I with a 6-0 win over San Marino last night with Aston Villa midfielder John McGinn hitting a hat-trick.
When the starting eleven was announced, Sheffield United fans were quick to notice that the 28-year-old did not even make the bench.
During the match, commentators confirmed that Fleck was ‘not fit for the bench’.
Fleck limped out of Sheffield United’s 1-0 win over Crystal Palace in August after picking up a knock to his hamstring.
Luke Freeman made his full United debut in the defeat to Leicester City a week later with the midfielder unable to recover in time.
Fleck then missed the 2-2 draw with Chelsea at Stamford Bridge before returning from injury in the 1-0 defeat home to Southampton following the international break.
He has played every minute of United’s next four Premier League games and will be hoping to return to action as the Blades host Arsenal on Monday, October 21.