Bhokanal clocked 6:59.89 to cover a distance of 2000m, little more than six seconds behind the third and last qualifier from the quarterfinal 4, Natan Wegrzycki-Szymczyk (6:53.52) from Poland.
Croatia's Damir Martin, the London Olympics silver medallist, won the quarterfinal with a far superior timing of 6:44.44, ahead of second-placed Alan Campbell (6:49.41).
Armyman Bhokanal, whose ailing mother is an Intensive Care Unit of a hospital in India, had clocked 7:21.67s in the Heats.
Bhokanal, the lone rower in fray from India, will now have to fight for the minor placings.