The Australian, who led England from 2015 to 2022, saw his young side swept aside in a nine-try rout as the hosts snapped a five-match losing streak.
When asked how he felt being back at the home of English rugby, Jones said: "It wasn't bad until some clown abused me going down the stairs at half-time.
"He said something but I'm not going to repeat it here because I'll get into trouble. Do you want me to get into trouble again? If there's only one clown in 81,634 that's not bad."
The Rugby Football Union reacted to the abuse of Jones by stating: "No coaches, players or match officials should be abused for doing their job."
Jones had avoided media duties earlier in the week but was characteristically outspoken when faced with questions over former England scrum-half Danny Care's criticsm of his management style.
In his autobiography, Care said that Jones oversaw a "toxic" environment and acted like a "tyrant" and "despot".
Responding to the allegations for the first time, the 64-year-old added: "I've got a new book deal. I just signed it today. It's going to be called 'Caring about Care' and you'll get all the details in there."
A convincing victory was much-needed for England coach Steve Borthwick after a difficult second year of his tenure.
England won just five of 12 Tests in 2024, including narrow defeats to New Zealand, Australia and South Africa at Twickenham over the past month.
"The overriding feeling this autumn is one of frustration to have come so close to getting results but not actually being able to convert them," Borthwick said.
"But there is real positivity around how the team played. I want the team to be brave with the ball, I want them to play fast, and we've seen growth in that area over the last four weeks.
"I'm really pleased with the way the players approached the game against Japan and the way they kept being disciplined to try and play the way they wanted to play for 80 minutes. You can see the identity they're trying to build as a team.
"In the last four weeks we've scored some really outstanding tries with the skill level that is in this group."
