Heffernan covered the distance -- about 31 miles -- in 3 hours, 37 minutes, 56 seconds. He was 62 seconds ahead of Russian silver medalist Mikhail Ryzhov with Jared Tallent, from Australia, coming in third at 3:40:03.
It was the first IAAF title for an Irish athlete since Sonia O'Sullivan won the women's 5,000 in 1985. The other Irish world championship gold was claimed by Eamonn Coghlan in the men's 5,000 in 1983.
Heffernan was second alongside leader Grzegorz Sudol from Poland at the halfway point of Wednesday's race and led, with Ryzhov in second by 1 second, at the 35km mark.
His lead was 2 seconds at 40 km and then he started pulling away, leading by 18 seconds going into the final 5 km and winning by more than a minute.
The 50km was the only final on Wednesday's schedule at the World Championships. There are six finals, including the women's 1,500, set for Thursday. The championships wrap up Sunday
The United States has four gold medals and five silvers -- both meet highs -- and one bronze for 10 overall medals. Russia is second with three golds and seven overall medals.