Sonatane Takulua (31) scored a hat-trick of tries as the Tongans claimed the final berth in Pool B, where they will face defending champions South Africa, Ireland, Scotland and Romania.
Hong Kong, who have never played at the World Cup, drop into a four-team repechage tournament alongside Kenya, the United States and Portugal for the last remaining spot at the tournament in France.
"I'm lucky enough to get these three tries, but it wasn't just me it was from all the boys and to get the win is a big relief," said Takulua.
The Tongans were dominant throughout, seeing two opportunities to open the scoring overturned by the video referee before William Havili slotted over a penalty for the Pacific Islanders.
Takulua extended Tonga's advantage when Solomone Funaki (28) bulldozed through the Hong Kong defence to set up the scrum half for the first try.
Hong Kong responded quickly when Gregor McNeish released Alex Post to score in the corner and reduce the deficit to five points, but the Tongans were soon back on the offensive.
Takulua claimed his second try from the back of a ruck on the Hong Kong try line before McNeish and Havili traded penalties after Tongan prop Siua Maile had been shown the yellow card.
Tonga highlighted the gulf in class in the second half, however, with Takulua completing his hat-trick soon after the restart.
Further tries from Sigfried Fisihoi, Telusa Veainu and Anzelo Tuitavuki extended Tonga's lead before Matt Worley grabbed two late consolation tries for Hong Kong.