The 35-year-old -- fourth in the event at last year's Olympics -- posted the fastest time of the year of 3hr 37min 56sec, with Russia's Mikhail Ryzhov in second (3hr 38:58).
Australia's two-time Olympic silver medalist Jared Tallent took the bronze (3hr 40:03).
Heffernan's gold is the first world title for the Irish since Sonia O'Sullivan's victory in the 5000 metres in Gothenburg, Sweden, in 1995.
It also came 30 years to the day since Eamonn Coghlan won Ireland's first worlds gold in the 5000 metres, in Helsinki.
"The final 10km of the race were as usual like a crucifixion.
"This victory is very important for me and for Ireland. I was fourth last year in London and this year I was not injured, I was in even better condition and was well prepared for this race."
Ivan Noskov and Ryzhov went out ahead together as they left the stadium with enigmatic Frenchman Yohann Diniz and Tallent chasing them.
The Russian duo -- who led the home challenge as Olympic and world champion Sergey Kirdyapkin did not start because of injury -- held a three-second lead over Tallent while Diniz was 10sec adrift at the 5km mark.
Noskov and Ryzhov upped the pace approaching the 20km mark, opening up a gap of about 100 metres on Tallent.
The Russians held a 9sec lead over Tallent and Diniz, who had joined the Australian, as they passed through 20km while Heffernan led the chasing pack some 22sec off the pace.
Diniz had the momentum as he left Tallent trailing and ate up the ground between himself and the Russians, joining them after 21km.
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