Exeter took the lead through Jon Challinor with four minutes left on the clock.
Scarborough looked buried as news of Forest Green's victory crept around the ground, but Tony Hackworth gave them a lifeline with an equaliser in injury time.
It set up a nail-biting finish as Scarborough threw everything at the Grecians but it proved too little too late.
Exeter started brightly and Matthew Gill forced goalkeeper Ian Dunbavin to save well with a fine strike from the edge of the box.
Lee Phillips shot wide early before Chris Todd headed the ball against the bar from a Billy Jones corner.
Scarborough, who needed a win to avoid the possibility of relegation, also had their chances in the first period.
Veteran Neil Redfearn fired over the bar and James Beadle almost gave his side the lead when his shot was headed off the line by Jones.
After the break Scarborough's Redfearn controlled the ball well inside the box before drilling the ball across the face of goal.
Exeter responded with a fine run and shot from the impressive Danny Woodards, which was well saved by the goalkeeper.
With four minutes remaining Exeter went ahead when Jamie Mackie picked out Challinor on the edge of the box and he stroked the ball past Dunbavin with a fine strike.
In injury-time Redfearn's corner was headed back by Beadle and Hackworth headed in at the far post. But it was too little too late and Scarborough were relegated.
Redfearn said: "It's not about what happened today, it is what has happened over the last few months. We were always playing catch up and we left ourselves too much to do."