Brentford centre-back Tony Craig headed into his own net unchallenged in the dying minutes after defensive partner Harlee Dean had done the same midway through the first half.
The own goals wiped out a brace from Paul Hayes, who opened his Brentford account when he fired home from close range after 11 minutes.
Pools clawed their way back into the game midway through the half when Antony Sweeney's cross was deflected past Bees goalkeeper Simon Moore by Dean.
The Bees, who dominated for long spells without ever really testing Scott Flinders, went ahead just before the hour when Hayes nodded home Clayton Donaldosn's right-wing cross.
But just as the points looked set to stay in west London Craig rose highest in his own box to loop a header in off his own post.