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The Welshman crossed the line 15 hours, 59 minutes and 29 seconds after winner Armel le Cleac'h who set a record time of 74 days, three hours and 35 minutes.
The 42-year-old Gosport-based Thomson's boat Hugo Boss crossed the line off the coast of France surrounded by a flotilla of smaller craft.
"Finishing this race is a result, but second is fantastic," he said.
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"I finished third last time so it's definitely a step up but it wasn't quite the first I was after.
"I've probably slept about five hours in the past three days and I haven't slept at all in the last 24 hours so I was running on the final bit of adrenaline left in my body.
"I've spent 70-odd days on my own and suddenly there's hundreds of people here and when I go in to the channel there's probably going to be hundreds of thousands.
"It's an amazing contrast and it's a wonderful way to finish."
Bangor-born Thomson was joined on his boat by his wife Kate and children Oscar and Georgia, and said their support meant he had never felt lonely during his epic journey.
"I didn't feel lonely - you can be in a large group of people and feel lonely," he said.
"I've got a beautiful wife and great kids supporting me - how can I feel lonely?"
Thomson matches Dame Ellen MacArthur as the best British competitor in the Vendee Globe. She finished second in the 2001 race.
His time is four days days faster than the previous race record of 78 days, two hours and 16 minutes set by Francois Gabart in 2012-13.
Thomson had threatened to overhaul Le Cleac'h on Wednesday, cutting his lead to 34 miles with 309 miles left of the race before a malfunctioning autopilot ended his challenge.
He had led for many of the early stages and broke two race records prior to being overtaken, with Le Cleac'h moving ahead in early December.
Thomson was nearly 1,000 miles behind at Christmas after his boat's hydrofoil was ripped off in mid-November, but he increased his speed after rounding Cape Horn.
He was leading the race by more than 100 miles when his boat was damaged.
Alex Thomson completed the 2016-17 Vendee Globe round the world race in second place on Friday morning.