The nation - only accepted as a member by FIFA in 1998 – reached their first major tournament thanks to Ashraf Al Fawaghra's stunning free-kick just before the hour mark in the Maldives.
Palestine are the 16th and final country to reach the Asian Cup and will join reigning champions Japan, Jordan and Iraq in Group D at the tournament, hosted by Australia.
The eventual victors controlled the match and deserved their success, with Khader Abuhammad going close in the early stages.
A rare Philippines chance saw Phil Younghusband fire over with only goalkeeper Ramzi Saleh to beat.
Palestine defender Haytham Theeb headed against the post nine minutes into the second half but his side did not have to wait much longer for the game's only goal.
Al Fawaghra provided it, curling a 25-yard free-kick into the top corner, and Palestine refused to sit on their lead as they went in search of a second.
One goal was enough, though, as Palestine's fifth clean sheet of the tournament sealed their spot at the Asian Cup.
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