Duns lost their third home game in a row, made all the more painful by a defeat for Ormiston at Hawick.
It all looked much brighter with just seven minutes on the clock when in-form Jordan Lauder netted after connecting in the box.
The visitors came straight back strongly and after home goalkeeper Paul Tansey pulled off a good save the visitors equalised after 29 minutes.
This temporarily spurred Duns on and on 35 minutes Conor Devaney had a good effort on goal after a good ball was played into the box, but at half-time it remained 1-1.
The second period commenced with both sides sparring for supremacy but Duns again displayed their Achilies heel by going behind to a 50th minute strike to give Burntisland striker Daniel Watt his second of the afternoon.
This is becoming a rather unpleasant habit for Duns.
Tansey again pulled off another great save with 67 minutes gone to just about keep the Dingers in the contest., but there was no further scoring and the visitors took the points.
Duns: Tansey, Weatherburn, Stewart, McHoul, Windram, D Brydon, Wales, Devaney (J Brydon 78), Lauder, Robinson, Waddell (Ainslie 82).