Striker Salim Toama scored the only goal in the second minute when he blasted a low, angled shot from 18 metres that skimmed the surface and beat Maccabi keeper Nir Davidovich.
Haifa dominated most of the possession during a largely disappointing final between Israel's two best teams over the past decade in front of 38,000 fans, but they rarely threatened Nigerian international goalkeeper Vincent Enyeama.
Haifa were seeking a second league and cup double 20 years after their first success but were unable to find a finishing touch to beat a strong Hapoel defence.
Haifa's defensive frailties almost saw them let in a second goal three minutes after the first when striker Ben Sahar shot wide. Veteran defender and captain Walid Badir then rattled Haifa's crossbar early in the second half and Toto Tamuz should have put the match beyond Haifa's reach near the end.
The victory was a watershed for Hapoel who are expected to revamp their playing staff next season, as coach Eli Guttman and many players appear set to leave the club, partly as a result of a financial dispute between the club's two main backers.
Haifa will play in the qualifying rounds of next season's Champions League and Hapoel will play in the Europa League qualifying rounds.
