National record holder Irfan was in the sixth position after the halfway mark and was maintaining his spot just before touching the 15-km point.
But Irfan, who had finished 10th in the 2012 London Olympics, was stopped by the race officials before the three-fourth mark for race rule violations.
His two compatriots Gurmeet Singh and Chandan Singh finished 33rd and 34th with timings of 1 hour 26 minutes and 47 seconds and 1:26:51 respectively.
Yesterday, Asian Games gold medallist Sudha Singh had failed to qualify for the women's 3000m steeplechase final round after finishing a disappointing 12th in her heat.
India are being represented by 15 athletes in the Championships.