The Mercedes driver had looked on course to challenge Max Verstappen for victory at Zandvoort after a strong run through much of the race, but the events were turned on their head by late VSC and safety car periods.
For the latter, Red Bull had elected to sacrifice track position to switch Verstappen to the softs while Hamilton was kept out on used mediums to take the lead with Mercedes feeling it was worth the risk in gunning for the win.
In the end, Hamilton was unable to hold Verstappen off at all as he was out-dragged from the final corner at the safety car restart and lost the front spot before the first turn.
While the Red Bull is widely known to have a significant straightline speed advantage over the Mercedes, the extent of the speed differential between the pair prompted some to think that there had been an engine problem at the restart.
But Hamilton insists that there was no fault and instead confessed to having initially accelerated in the wrong engine mode, which would have cost him momentum compared to Verstappen behind him.
"I was late to get to race mode, but I was on race mode on the straight," he said. "They were just so fast on the straight."
The radio conversation between Hamilton and his engineer Peter Bonnington at the time shows that Hamilton was reminded before the end of the safety car period to change his engine mode into its balanced race setting, Strat Five.
Bonnington told him: "So when the lights go out it will be Strat mode five," he said. "You can use an early overtake push, push and hold available at your discretion."
As Hamilton accelerated through the banking of the final corner to go for the restart, Bonnington again came on the radio to remind him about Strat Five, as Hamilton was initially without the 160 horsepower boost available from the MGU-K for around one second until he flicked over.
Ultimately, however, the engine mode delay made little difference to Hamilton's prospects of holding Verstappen off, as the Red Bull's top speed would have been too much to keep him back anyway for more than a couple of laps.
Mercedes boss Toto Wolff said after the race that the top speed problem was why there was no expectation of being able to challenge Verstappen from behind on equal tyres.
"I think what we need to look at is that we're lacking straightline speed," he said. "Our car is too draggy. And before we fix that, it's going to be very difficult to fight with them on the straight line, especially on a track where it's difficult to overtake.
"You never say never. But the probability [of being able to overtake the Red Bull] is less than 50%."