The country's last pager provider, Tokyo Telemessage, closed its service on Tuesday.
Fewer than 1,500 subscribers remained, most of them health workers.
The last private subscriber was said to be a man who kept his pager because it was his 80-year-old mother's preferred way of contacting him.
On Sunday, a Tokyo funeral company set up a tent near a railway station, so people could lay flowers and pay their respects to the end of the pokeberu, or pocket bell.
A photo of a pager displayed the message "1141064", Japanese pager code for "we love you".
Developed in the 1950s and 1960s, pagers grew in popularity in the 1980s. By 1996, Tokyo Telemessage had 1.2 million subscribers, with 10 million subscribers nationwide, according to the Kyodo news agency.
As well as workers, they were popular among high school students, who used numerical code to exchange messages. But soon after the peak, the mobile phone arrived, signalling the end of the pager era.
Despite being the birth-place of tech giants such as Nintendo, Panasonic, and Sony, old technology habits can die hard in Japan.
In 2015, the BBC reported that faxes and tape cassettes were still common, while last year, a government minister admitted he had never used a computer.
The politician in question, Yoshitaka Sakurada, was cyber security minister at the time.
"Since I was 25 years old and independent I have instructed my staff and secretaries," he said. "I have never used a computer in my life." Reuters