After a quiet opening spell Elgin created a first opening when a jinking Andrew Roddie run created some space for Martin Harty but the striker's half hit shot was no test for Andrew Carlin.
Midway through the half Elgin took the lead. Once again Roddie and Harty combined with the latter beating two men before rolling it into the path of right winger Craig Higgins, who drilled it low into the bottom corner of the net.
City very nearly doubled their advantage on stroke on half time when Harty was fortunate to see his attempted back-heel fall back into his path, but from six yards he smashed his shot off the cross bar.
The second half began with Elgin on the front foot and a well worked move between Harty and Higgins created space for the goal scorer, however, a fine block by Innes Ritchie kept it at 1-0.
Elgin went close again in the 65th minute when Higgins' drilled centre was only cleared as far as Adam Nelson who controlled the ball, shot and turned in one movement only to be denied by the nearest of deflections.
Fraser Bremner then tried his luck from 25 yards with a fiery effort that Carlin did well to tip over the bar.
The Blues had been anything but Brazilian up until now; however, they came close to levelling twice in the space of three minutes with what were their only efforts at goal.
Firstly a high ball into the box saw Kieron Renton miss his punch under pressure, but Nelson spared his blushes clearing Calvin Shand's effort of the line.
Elgin City wrapped up the win two minutes from time when striker William Martin charged down the Cowdenbeath keeper's attempted clearance and duly rolled the ball into the empty net.