“This was his last World Championships, his last chance," said Lefevere, who has managed the Belgian at the QuickStep squad for almost the entirety of his career.
“He put everything into this race, had really counted on it. And then it didn’t happen,” he told nieuwsblad.be.
“In thirteen, fourteen years, I’ve never seen Tom so disappointed.”
Lefevere admitted that it was “perhaps” too much for Boonen, going up against Peter Sagan and Mark Cavendish in the sprint finish on Doha's Pearl island.
“Tom was also a bit early in second position. But given the circumstances, it was very difficult to make more out it,” he said, adding that Sagan, who made it back-to-back world titles, is "the best rider in the world".
The 61-year-old manager also had praise for the Belgian team in general, who had vowed to try and shape the race in the desert and make things as tough as possible.
“They took him [Boonen] to the line, didn’t make any difficulties for him," said Lefevere.
“But what was the alternative? In hindsight it is always easy. And you certainly can’t complain that the Belgians were not brave. Many countries rode passively, but they took the race into their own hands.”