The incident occurred in the 18th minute as Scott collided with Basingstoke player Nana Owusu. The Slough stopper was treated on the Arbour Park pitch for around half an hour before an ambulance arrived. Scott was taken to Wexham Park Hospital and it was confirmed that he had a broken bone in his neck.
Without a second goalkeeper on the bench, Slough battled on with midfielder Gurkan Gokmen taking the gloves - and ground out a result which keeps them firmly in the hunt for a playoff place.
The Rebels had the lead when play was stopped, with Chris Flood's unchallenged eighth-minute volley from a James Dobson corner breaking the deadlock after the home side had shaded the early exchanges.
Slough continued to cause panic in the Basingstoke box with corners delivered by Dobson, and twice the ball found its way through a crowd of bodies and away to safety.
After the lengthy delay, Basingstoke carried a greater threat and tried to test Gokmen as quickly as possible, but Sam Deadfield fired over the bar on his left foot.
Minutes later, Slough doubled their lead when two former Dragons players combined. Manny Williams received the ball six yards out and touched the ball to an unmarked Flood to side foot past Alex Tokarczyk.
Flood had two opportunities to complete a first half hat-trick, heading a Sean Fraser cross over the bar before firing into the midriff of Tokarczyk after Deadfield had dragged a shot wide at the other end.
And the Rebels really should have put the game beyond doubt early in the second half, with Williams unlucky twice not to get his name on the score sheet. First he curled a shot with his left foot which rebounded back off a post, and then a minute later he rounded Tokarczyk only to see his shot cleared off the line by Joe Gater.
From the resulting corner, Mark Nisbet was also inches away from scoring, but he volleyed just wide of the post.
Instead, Basingstoke pulled one back on 55 minutes as half-time substitute Aaron Redford followed up to score after stand-in keeper Gokmen fumbled a swerving free kick attempt from Owusu.
Despite the need to protect their goalkeeper, Slough still carried the greater attacking threat. After Dobson fired wide from 20 yards, Tokarczyk got down low to save from Simon Dunn after being teed up by the industrious Williams. Minutes later, Dobson was inches wide with a bending effort which flew just past the post.
The visitors caused plenty of nervous moments as pressure increased on the Slough goal, but the Rebels stood firm with Gokmen called upon to save from Redford with a foot before diving onto the loose ball, and then he claimed the ball following an effort from Aaron Jarvis.
However with fifteen minutes left, Dobson relieved the pressure with a third Slough goal. The winger’s 20th of the season was a trademark effort as he bent a left-footed shot into the far corner of the goal moments after seeing a strike beaten away by Tokarczyk.
But back came Basingstoke, and Redford scored his second, blasting the ball over Gokmen after a defensive error, leading to a nervy end to the game.
Slough did their best to eat away at the remaining time to see out the game, and had to withstand one final free kick delivery after a foul out on the touchline from Fraser - but the ball dropped wide of goal and the Rebels’ gutsy performance saw them through.
Basingstoke Town Line up
Alex Tokarczyk, Marcus Johnson-Schuster, George Bennett, Dan Collier, Joe Gater, David Ray (c), Sam Deadfield, Charlie Kennedy, Aaron Jarvis, Ashleigh Artwell, Nana Owusu. Substitutes: Aaron Redford, Kieron Greene, Michael Atkinson.