Ashraf Nu'man Al Fawaghra's solitary strike coming from a well-taken free-kick in the second half proved to be the winning goal in Maldives.
A clean sheet in the final also ensured that Palestine ended their AFC Challenge Cup campaign having conceded no goals in the four matches played at the competition.
Their goalless draw against host nation Maldives was the only instance the West Asian state failed to find the net, having registered 1-0 and 2-0 wins over Kyrgyzstan and Myanmar respectively in the group stage, before seeing off Afghanistan in the semi-final
Philippines, meanwhile, were the only south-east Asian team left in the competition following the group stage exits of Myanmar and Laos.
Maldives finished in third place after defeating Afghanistan 8-7 on penalties, following a 1-1 result at the end of extra-time on Thursday night.
The qualification marks Palestine's first appearance at the Asian Cup where they will be placed in Group D alongside Japan, Jordan and Iraq.