The Suphanburi FC midfielder was left out of the original party but the 27-year-old was called up as a late replacement for Pinyo Inpinit, one of three over-age players in the under-23 squad.
Jakkaphan, the most experienced player in the squad, joined his team mates in Bangkok on Monday ahead of a training camp in Phuket for the September 19-October 4 Games only for the Olympic Committee of Thailand to reveal his ineligibility.
The body said Jakkaphan's name was not on the list of 40 registered with the International Olympic Committee.
"It's a pity that Jakkaphan can't play for us. His experience would have been valuable for the team," the team's coach Kiatisak Senamuang was quoted as saying by Thai media.
"I talked with him and he understands the situation. I will now call Pinyo back into the team."
Thailand have been drawn in Group C alongside Indonesia, East Timor and the Maldives as they aim to win a first Asian Games medal in soccer after three fourth place finishes.
Failing to properly register players really hit the headlines earlier this month when Legia Warsaw were kicked out of the Champions League for failing to properly register a suspended player before playing him briefly at the end of a 6-1 aggregate win over Celtic.
- Sports & Recreation
- Olympic Committee of Thailand