FIFA's appeals panel awarded Palestine a 3-0 victory in the teams' first-leg match in February, which Thailand had won 1-0.
Thailand midfielder Sucharit Chanthakul played while still suspended for a red card he received at the 2008 Asian under-19 championship.
After Palestine won the return match 1-0 in the West Bank, Thailand advanced after a penalty shootout.
FIFA's ruling gives Palestine a 4-0 aggregate victory.
Palestine next plays Bahrain. The June 23 return will be only the second competitive international played on Palestinian soil.
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