What was even worse he'd overslept.
Thomson -- who like many sailors sleeps in 20-minute bursts throughout the day -- had forgotten to charge his shockwave watch, specially designed to release an electric shock to wake him up.
Instead, the 44-year-old from Gosport, England awoke to the thud of a damaged stern, bow and foil on the starboard side of his 60-foot Hugo Boss yacht -- and the pangs of a broken heart.
"It's a real shame for me and the team to be in the position that we are in," an emotional Thomson told reporters on Friday.
With no choice but to start his engine to escape the rough terrain, Thomson triggered a 24-hour penalty and has all but dashed plans for a champagne celebration.
Although he crossed the finish line in Pointe-a-Pitre on the Caribbean island of Guadeloupe first on Friday, the penalty means Thomson will likely place out of the top three finishers of the race which began on November 4 off the coast of Saint Malo, in northern France.
"The jury has decided that I have a 24-hour penalty which will mean I will not win the race," he accepted.
"How do I feel about that? Well, I think that is very fair because I don't think I should win the race after hitting Guadeloupe."
'They don't think you're coming back'
Thomson finished second and third in consecutive Vendee Globe around-the-world solo races. He spent an astonishing 74 days at sea in the 2016-2017 edition.
"In some ways it's easier because it's not quite as daunting," Thomson told CNN Sport days before embarking on the Route du Rhum, "but on other hand, there's no downtime and you can't make a mistake -- so it's a bit unforgiving,
"You're still racing across the Atlantic on your own. The Vendee Globe is almost gladiatorial -- half a million people turn up at the start, probably because they don't think you're coming back.
"This one, I don't think about not coming back. I think about drinking rum in the Caribbean in a few weeks.
"It's a different challenge, but it's not a leisure cruise. The boats have become faster and faster, in theory it's a downwind race which is pretty stressful, there's no time to get into a rhythm and you'll be more tired than ever before."
That talk of fatigue proved prophetic and spelled Thomson's undoing.
Thomson planned to sleep in 20 to 40 minute bursts every two to four hours during this race, and made note of an alarm clock wired to a loud horn to wake him up.
In case he was still asleep five minutes later, the shockwave watch was designed to deliver a mild but "not very pleasant" electric shock.
Sadly, that system failed when Thomson slept right through the horn on Thursday, and the modern-day risk of not charging one's digital device caught up to him.