Following an independent disciplinary process, the 66-year-old Australian - a former England and Australia coach - accepted the decision. His suspension runs from April 24th to June 5th.
Jones will be barred from attending or taking part in four matches, including Japan's Nations Championship opener against Italy in Tokyo on July 4th.
"Some inappropriate remarks that I made caused discomfort to local match officials and other related parties," Jones said in a statement.
"I would like to offer my sincere apologies to everyone involved. I deeply regret my behaviour and words and will make every effort to ensure that this doesn't happen again."
Jones returned as Japan's head coach in January 2024, having previously led the Brave Blossoms from 2012 to 2015.