Tom Owen-Evans put the Bulls ahead in the 13th minute but Josh Gowling's side failed to put the game to bed and the Urchins scored three second half goals, their last two coming in the final four minutes.
It is the second time Hereford have lost at Wembley after losing 4-1 to Morpeth in the Vase Final, which was exactly five years ago. The Bulls also took the lead in that game.
Due to coronavirus restrictions, only 3,000 fans were able to watch Hereford compared to at least 20,000 that went in 2016.
There were no surprises in the Hereford line up and it was nice to see Joey Butlin, the goalscoring hero from thre semi final, starting after it emerged he was a slight doubt. Luke Haines, who has now signed permanently, also started.
Hornchurch had an early chance before Hereford took the lead in the 13th minute. A short corner led to Chris Camwell setting up Owen-Evans, who slotted the ball home via a deflection.
Hornchurch posed little threat in the first half and really that was Hereford's opportunity to kill the game off. Butlin headed wide before Michael Bakare's delicate chip went over. Camwell also had an effort at the goal as Hereford went into the break deserved winners.
But instead of 'going for the jugular' the Bulls sat back in the second half and, while only a goal behind, Hornchurch were always in the game.
As the half wore on, they gained more confidence and exerted more pressure.
Hornchurch almost levelled when Liam Nash beat the offside trap and slotted the ball past Brandon Hall in the Hereford goal. However, Bulls captain Jared Hodgkiss came to the rescue, clearing the ball off the line.
However, Hornchurch did level 15 minutes from time when Charlie Ruff was on hand to tap home after Jamie Grimes headed the ball on to his own bar.
Kyle Finn and Bakare then had efforts at goal at the other end as Hereford fought to regain the lead, but it was Hornchurch who got the all imporant third goal of the match in the 86th minute. Nash, who was named man-of-the-match, showed great composure to fire the ball home after it fell to him nicely inside the box.
That goal sucked the life out of the Hereford, and you could sense the Bulls fans thinking 'here we go again'.
And indeed it was when a Hornchurch sealed the win in stoppage time when Ellis Brown broke clear to beat Hall. At the final whistle, some Urchins fans invaded the pitch while their boss Mark Stimson 'had words' with Bulls assistant manager, Steve Burr.
Hereford: Hall, Hodgkiss, Haines, Grimes, Camwell (McQuilkin 74), Butlin, Owen-Evans, Finn (Kouhyar 88), Lloyd, Bakare (Klukowski 90), Butroid. Subs not used: White, Pollock, Digie, Jones.
Hornchurch: Wright, Parcell, Hayles, Clark, Sutton, Muldoon, Spence (Ruff 59), Christou, Brown, Higgins (Dickson 59), Nash (Stimson 90). Subs not used: Thackaway, Winn, Hassan, Cooper.