The feat by Darren Sarll's youngsters was even more impressive as Boro found themselves 3-1 down at one point, only to mount a comeback and clinch victory with a last minute winner.
After falling a goal behind Ben Kennedy equalised, only for two further strikes to give the Hornets a comfortable lead. However a Dale Gorman penalty and another strike from Kennedy, his 13th of the season, levelled matters before George Casey won the game late on.
The result means Boro need to beat Luton at home on Saturday to guarantee qualification for Merit League 1, which sees the top seven teams in the South-East division play the top four teams in the South-West division. The remaining teams in both divisions play each other in Merit League 2.
Should both Leyton Orient (who at at home to Southend) and Stevenage win, the final spot will be decided by goal difference and Stevenage currently have a five goal advantage. Northampton, who are at home to MK Dons, could benefit if either Boro or Orient slip up.
Kick-off tomorrow morning between Stevenage and Luton is 11am at Shephalbury, so if you're not making the trip to Shrewsbury why not go down and back the Boro youngsters!
Stevenage: Reading, Casey, Smyth, Johnson, Jackson, Gorman, Kerr (Bruce), Kennedy, Storer (Butaka), Sweeney (Yamfam), Akinyemi
Subs not used: Jones, Trialist