The nervy Shots could have taken the lead early on, but Dwain Clarke somehow skewed his shot way over the bar from just two yards out.
At the other end Neil Redfearn was also off-target for the Seadogs.
Then an unbelievable scramble in the Boro box saw Brett Johsnon and Will Antwi have efforts, only for keeper Leigh Walker to somehow block them both.
Shots keeper Nikki Bull denied Tony Hackworth from close range before the Shots took the lead. Sills heading home from Darren Barnard's corner.
The second half saw the Shots take control of the game with Sills and Nick Crittenden just off target. The home side were all over Scarborough who had little to offer in return.
Nick Crittenden burst through only to see his shot blocked by Colin Cryan.
Sills then headed straight at the keeper before finding the target with five minutes left on the clock.
Tarkan Mustafa stole in towards the area and crossed in for Sills so strike past the defenders on the line for 2-0 and ease the tension of the Shots supporters.
Gary Holloway shot just wide of the post and sub Jamie Slabber hit the post after Jon Challinor's ball in, but it did not matter as the Shots had done enough to secure victory and a spot in the play-offs for the second year running, this time to face Carlisle United.