Eekhoff - who crashed early on before catching up with the peloton - was part of a three-man group which remarkably caught up with four riders in the final kilometre of the 173km Doncaster to Harrogate route.
'Illegal drafting' - The incident which led to Nils Eekhoff's disqualification
The seven riders then sized each other up ahead of the sprint to the line, but it was Eekhoff who squeezed over the line first, with Samuele Battistella (Italy) claiming silver and Stefan Bissegger (Switzerland) bronze.
Great Britain’s Thomas Pidcock finished an agonising fourth, with Sergio Andres Higuita Garcia (Colombia), Andreas Lorentz Kron (Denmark) and Tobias Foss (Norway) also missing out on a podium spot.
However, Pidock was then bumped up to bronze, as Battistella was crowned the champion with Eekhoff disqualified after a review of the race footage by the UCI commissaires.
The World Championships website confirmed that Eekhoff "had illegally drafted behind a team car to get back into the bunch after an early crash", while a UCI report stated it was for "sheltering behind or taking advantage of the slipstream of a vehicle".
The team behind Eekhoff will reportedly fight the disqualification.
The thrilling seven-way sprint before Eekhoff's DQ
Pidcock was caught up in a crash earlier in the race and required a bike change before catching up with the pack. As the riders tackled Greenlow Hill, wind split the pack and riders caught up with the breakaway.
The 24-man lead group became six when Bissegger, Foss, Battistella, Pidcock, Idar Andersen (Norway) and Szymon Sajnok (Poland) all motored ahead.
Andersen suffered an agonising puncture with 14km to go before the final circuit, and it was then a five-way fight for gold as they extended their lead over the chasing pack.
Eekhoff talks through thrilling final moments before his DQ
With 6km to go, Sajnok faded before Bissegger veered into Battistella’s front wheel while looking back.
Bissegger was unclipped but managed to keep up as Battistella gave the Swiss a stern look, but it was then all eyes on the finish with the chasing pack catching up.
Eekhoff DQ bumps GB's Pidcock up to bronze on dramatic day
A 14-second gap with 4km to go crept under 10 seconds over the next kilometre which was then halved with 2km to go.
The quartet were eventually caught up, and it was Eekhoff who saw off the other six to claim the rainbow jersey - or so he thought.