Some good work in the middle of the park failed to create any clear cut chances early on with Scott in goal for the visitors having little to do.
Midway through the first half Heriot Watt started to get into the game and should have taken the lead when Lukowiecki blasted over the bar.
Coldstream failed to learn a lesson from this when a similar move on 25 minutes saw the visitors take the lead. A Watson shot from 12 yards gave Lumsden no chance after good work by Lukowiecki down the left.
The home side then stepped up their work rate, excellent work by Gibbard produced a good cross that Simpson headed narrowly wide, and then a low shot from Chisholm was just beyond Wales as he slid in at the far post.
The home side ended the half the strongest but still a goal down.
Coldstream continued to press after half time, a Bolton shot going just wide, then an Inglis shot was deflected for a corner.
As the half wore on Coldstream became more frustrated at their lack of success in front of goal, even a change in personnel had little effect, although James Brydon did force a sharp save from Scott at the base of the post.
In the dying minutes, a now less than convincing Coldstream found themselves short of cover at the back as Napier scored a simple goal to secure the win for the students.
Coldstream: Lumsden, Tyson, Renton, Brown, D. Brydon, Bolton, Inglis, Chisholm, Wales, Gibbard, Simpson Subs: J. Brydon, Burns, Agnew, Travis, Shepherd, Cowe.
This Saturday Coldstream will entertain Edinburgh University at Home Park in a match which was to have been played in Edinburgh but was switched as the University facilities have been hit by flooding.
Eyemouth United's match against Tynecastle on Saturday was postponed at the last minute due to the weather. On saturday the Fishermen will host Kelso United in a Borders derby.