Second-half strikes from Barry Corr and Britt Assombalonga secured Phil Brown his first win as Shrimpers boss yet left the struggling hosts teetering four points adrift of safety with just two games remaining.
However, Scott - who took charge at the EBB Stadium in February - claims the Shots' five-year stay in the Football League is not necessarily over.
"It's not over yet," said Scott. "If we have that level of performance and that level of commitment then it's not over. The boys gave everything; I could not have asked for more.
"We need to win our last two games and we will be going all out to do that, like we did here. We desperately wanted to win this one and we desperately tried. We did everything we could and we'll do it again.
"I've never given up on anything in my life, and the fans were great. They saw a team that was doing their best.
"We dominated the game and we've got nil again. We have not tested their goalkeeper enough. It's the story of our season."