Down 25-9 at the break, Japan stormed out of the gate and outscored Canada 25-0 over the final 40 minutes to stun the hosts 34-25 in the first game of the Pacific Nations Cup tournament for both countries.
Jones is back coaching after suffering a stroke in October, but that didn't stop him from letting loose on his players after a disappointing first half.
"I'll tell you what, it wasn't good for my blood pressure," said the 54-year-old. "We thought we were fitter than them. We thought if we could just hang in there ... we were just like a boxer on the ropes hanging on there. And if you get a chance to throw a jab, you throw it, and that's what we were able to do.
"It takes a bit of courage to do that, so I'm really pleased with that from the boys."
Japan ran ragged in the second half, busting through the line for a pair of tries that left Canadian head coach Kieran Crowley shaking his head.
"We really played well in that first half. We put pressure on them, we scored a couple really good tries," he said. "Second half, we had a couple bad defensive errors from set plays, which you can't afford to do. They were pretty soft tries, really.
"Japan just took it to us and they deserved to win with that second-half performance."
Yoshikazu Fujita, Yu Tamura and Hendrik Tui had the tries for the visitors, who won their eighth straight overall, while Ayumu Goromaru kicked five penalties and added two converts.
John Moonlight, Ciaran Hearn and Taylor Paris had the tries for Canada, while James Pritchard added two penalties and two converts.
Japan started to claw its way back after halftime with a try in the 42nd minute as Fujita dove over the line, and after Goromaru missed the conversion, the score stood at 25-14.
Goromaru then kicked his fourth penalty of the night in the 56th minute to make it 25-17 before Tamura broke through the Canadian midfield untouched in the 63rd, with Goromanu's conversion cutting the deficit to just one.
Clearly rattled, Canada could barely hold onto the ball and Tui completed the comeback by again busting through the line to make it 31-25 after Goromaru's conversion.
Goromaru added to his point total by booting another penalty on the last kick of the game for the 34-25 final.
"We always knew we'd have to cope with the physical onslaught of Canada at home for the first 40," said Jones. "If we wouldn't have given away that try away (before) halftime we would have been pretty happy, but 25-9 at halftime, you're battling to stay in the game."
Despite watching his team get bossed around in the second half, Tyler Ardron — a 22-year-old from Lakefield, Ont., who plays for Ospreys in Wales and captained Canada for the first time — saw some positives.
"Tons of things to work on still," said Ardron, who made just his 14th appearance for the national team. "But we executed a lot things that we wanted to and I think if you look at that first half, a lot of things went our way and in the second half a couple bounces maybe went their way."
The six-team Pacific Nations Cup tournament also includes Samoa, Fiji, Tonga and the United States. Canada will play world No. 10 Scotland at Toronto's BMO Field next Saturday before travelling to Sacramento, Calif., to face the U.S. on June 21 in another Pacific Nations Cup match.
The tournament consists of two groups of three teams, with each country taking on the other two in its conference. The top teams from each meet in November's final.
Before his team's dominating second half, the turning point appeared to come in the 34th minute when Japan's Shota Horie was sent to the sin bin for a foul, leaving his team down a man.
Pritchard made the ensuing penalty from close range and Canada opened the floodgates with two impressive tries to close out the half.
Moonlight finished off a good move for a try in the 37th minute before Paris broke through the Japanese line moments later, with Pritchard converting both for a 25-9 lead.
"(We) definitely didn't think it was over," said Ardron. "I think we felt that if we played our game over the next 40 minutes we would be comfortable, but that clearly wasn't the case.
"Credit to Japan — they came out and played their game and we didn't turn it around."
Japan, ranked No. 12 in the world, has been a pain for 15th-ranked Canada over the last several years. The Japanese tied Canada at the last two Rugby World Cups, with the 23-23 draw in 2011 helping to push the Canadians to fourth in their pool to miss out on automatic qualification for the 2015 tournament.
Japan then beat Canada 16-13 in last year's Pacific Nations Cup, a result that handed the championship trophy to Fiji.
Crowley said earlier in the week that a win over Japan on home soil would help propel his side up the International Rugby Board's rankings and his players started brightly in front of a partisan crowd at Swangard Stadium.
Canada had sustained pressure early in the match, with Hearn going over the line for the opening try in the seventh minute, but Pritchard missed the conversion for a 5-0 lead.
Goromaru got Japan on the board with a penalty kick in the 12th minute, and he connected again three minutes later to give his team a 6-5 advantage.
Pritchard then added a penalty in the 18th minute to restore the Canadian lead at 8-6, but Goromaru kicked his third penalty of the half in the 29th to make it 9-8 Japan.
"Rugby's on a bit of a high at the moment in Canada," said Crowley. "We've just got to get some of these tight games across the line. Japan have had our number a little bit the last few times we've played them, which is unfortunate."
Notes: Scotland beat the U.S. 24-6 on Saturday night in Houston. ... Saturday marked the first time Canada's men's team wore its new uniforms designed by Under Armour. ... Japan meets the U.S. in Carson, Calif., next weekend. ... Attendance was 6,382.