IPC President Andrew Parsons sounded a note of unity at the ceremony in the Olympic stadium after athletes from Russia and Belarus were expelled earlier.
The about-face came less than 24 hours after the International Paralympic Committee announced it would allow Russians and Belarusians to compete when the Games open on Friday.
The two-person team of Zakia Khudadadi and Hossain Rasouli had flown from Kabul to Paris before continuing on to Tokyo, the International Paralympic Committee said.
Two Para athletes were scheduled to compete in the Games -- taekwondo athletes Zakia Khudadadi and Hossain Rasouli. Khudadadi, 23, was to be the first woman ever to represent Afghanistan.