Eekhoff was the fastest in the drag race to the line after an exhausted front group made it to the finishing straight with 40 seconds advantage on a chasing group after weather and hard racing had made sure that only the strongest were present in the final group.
It looked like it might be a hometown win for cyclocross star Tom Pidcock (Great Britain), but the big Dutch rider was able to rally in the final metres to cross the line ahead of a fast-finishing Samuele Battistella (Italy), who was to be elevated to the gold medal after Eekhoff's disqualification.
Stefan Bisegger (Switzerland) moved one step up the podium into the silver medal, while home star Pidcock moved onto the bottom step as the third-placed finisher.
Australia's best finisher was the Mitchelton-Scott-bound Kaden Groves, who ended up in the second group, coasting over the line for 14th after suffering a late mechanical.
After the race, the celebrations of Eekhoff and the Dutch team were unbridled, but the news slowly came through the race jury were considering footage of an incident during the race. Eekhoff had crashed with about 130 kilometres remaining, dislocating his arm and breaking his bike before getting his arm put back in, remounting on a spare and spending a few minutes behind his team car in returning to the peloton.
The race jury decided that was too much assistance and disqualified the now distraught Eekhoff. The Dutch cycling federation did not appeal the decision.
"They showed me the footage and said they hadn't made their decision – they just wanted to show it and I could say my thing," said Eekhoff. "Then I went back to the tent, and I saw Pidcock was already there, so I was like 'ok'. Then one minute later they told me I was disqualified because of the image of cycling."
"I just started crying. I felt helpless. I had no idea what I could do.
"They just left me in the tent. They left, and I was sitting there. I just wanted to go home."
Eekhoff's management team SEG cycling have looked to take the matter further, and may exercise legal options to force the UCI to reinstate Eekhoff as the world champion, but nothing has been officially announced yet.
It was the opposite emotion for the elevated Battistella, whose day just got better after his silver medal got converted to gold and he wore the coveted rainbow stripes on the podium.
"I don't have the photo with the hands up but now the sensation is very good," said Battistella. "I'm sorry for the rider (Eekhoff), I was happy with second place but now I'm the world champ. I can't believe it... it's fantastic.
"Here there are the strongest and in Yorkshire 99 per cent is rain. I was prepared for this, I know my form, I know my legs and I can't believe it, I'm the world champ. Maybe I will sleep with the jersey tonight and tomorrow morning I can understand what happened today."