The Blue Brazil are now just one point behind second placed Berwick with a game in hand and even leaders Stenhousemuir could yet be caught.
But the outlook was less sunny two minutes before the break as Cowdenbeath trailed 2-1 before a quick-fire double from striker David McKenna - his third and fourth goals in two games - swung the match in their favour.
Elgin had earlier made the breakthrough following a poor opening period when Adam Nelson's short pass set up Martin Johnstone for a delicate low finish.
Cowdenbeath soon levelled through a typically fierce drive from recent signing Armand One, although schoolboy defending then allowed Nelson's free-kick to float towards the back post where Mark Booth steered the ball home to make it 2-1 to the visitors.
Both of McKenna's goals were created by top-scorer Liam Buchanan and were expertly finished.
Then defender John Ward opened up some daylight early in the second half with a looping header from a Graham Guy corner.
Substitute Mark Baxter hit the woodwork with an outrageous effort from 35 yards and McKenna was denied his hat-trick by a goalline clearance before Iain Mauchlen completed the scoring nine minutes from time with a shot which flew high into the roof of the net.