Bouchart, who pressed the button allowing the lorry to leave, said it was a "historic moment" adding that going back to customs checks after the UK's near half century of European Union membership "will have consequences whose range we don't yet know".
It has been 4 1/2 years since Britain voted in a referendum to leave the bloc it had joined in 1973.
The end of the transition period, four-and-a-half years after a majority in the United Kingdom voted to quit the European Union, is a significant moment in the nation's history.
He spoke after haulage firm announced plans to temporarily suspend its European services in the new year to judge whether they will become "mission impossible" after the Brexit transition period ends. England and Wales voted out but Scotland and Northern Ireland voted in.
Scotland's First Minister Nicola Sturgeon said the European Union should be ready to welcome an independent Scotland back into the bloc.
But the turmoil of the euro zone crisis, attempts to integrate the European Union further, fears about mass immigration and discontent with leaders in London helped Brexiteers win the referendum with a message of patriotic, if vague, hope. "We are relieved because we know how we will work", he said.
Supporters see Brexit as an escape from a doomed Franco-German project that has stagnated while the United States and China surged.
This means that Britons lose their ability to freely travel and work in the 27 nations included in the bloc.
Boris, now hailed as the conquering hero by hardline Brexiteers in British politics, has written an exclusive new year's article for the Daily Telegraph, in which he said: "But before you shoot your head back under the (duvet) covers - let me offer some grounds for thinking that this New Year really is a year of change, and hope".
Sturgeon has said that if her Scottish National Party wins elections to Edinburgh's semi-autonomous parliament scheduled for May, an independence referendum should take place quickly. More red tape means more cost for those importing and exporting goods.
Passports must be valid for more than six months, visas or permits may be needed for long stays, pets need a health certificate and drivers need extra documents.
Previous night observed a range of European countries - which include Italy, Portugal, Norway and Poland - area new limitations on travellers arriving from the Uk in effect from January 1, with exemptions only for those people with necessary reasons to travel.
"It's good to see the port's done its job and there's no backlog", Alan Leigh, 52, told AFP while taking an early New Year's Day stroll on the famous white cliffs above the Dover docks as the ship left on the outbound trip.
"We figure it gives the country a week or so to get used to all of these new systems in and out and we can have a look and hopefully resolve any issues in advance of actually sending our trucks", said Youngs director Rob Hollyman.
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