Less than 6,000 Tangerine supporters made the trip to the capital due to a protest against their owner and chairman, but they were given something to cheer about after just three minutes.
Mark Cullen – who netted a hat-trick in Blackpool’s semi-final first leg triumph over Luton Town – produced a classy touch and flick to find Brad Potts who found the bottom corner.
Exeter rallied as Ollie Watkins was denied by Sam Slocombe before David Wheeler collected a long ball forward and lobbed the keeper to deservedly draw the Grecians level five minutes before the interval.
Blackpool had numerous chances to retake the lead after the break and did so in the 64th minute.
Goalscorer Potts repaid Cullen for his earlier service by delivering a low cross for the striker to prod home with his studs from close range.
Paul Tisdale’s Exeter side had opportunities to take the game to extra time late on but Blackpool held on to seal promotion to the third tier of English football.