The deal, unveiled last month, means nearly all its exports to Japan will be tariff free while removing British tariffs on Japanese cars by 2026.
UK International Trade Secretary Liz Truss called it a "ground-breaking, British-shaped deal".
But critics have said it will boost UK GDP by only 0.07%, a fraction of the trade that could be lost with the EU.
The two countries had reached a broad agreement in September, and the deal is expected to boost trade between the UK and Japan by about £15bn.
The deal, which was negotiated over the summer, will take effect from 1 January 2021.
But some experts said it was a missed opportunity between the UK and its 11th biggest trading partner.
International Trade Secretary Liz Truss had struck the deal with Japan's foreign minister Toshimitsu Motegi on a video call on 11 September.
After the ceremony, Ms Truss said: "How fitting it is to be in the land of the rising sun to welcome in the dawn of a new era of free trade." She added it would "pave the way" towards UK membership of the wider Trans-Pacific Partnership.
Ms Truss had earlier hailed the importance of the agreement.
"At its heart, this deal is about creating opportunity and prosperity for all parts of our United Kingdom and driving the economic growth we need to overcome the challenges of coronavirus," she said.
Source: Financial Times