The former Rochdale striker nodded home an injury time equaliser to banish almost 18 months of injury misery since joining the Bees.
The 24-year-old tore his cruciate in only his second game for the west Londoners and then suffered a re-rupture near the end of his rehabilitation.
So when he stepped up to take a penalty that he had won with six minutes to go, his side trailing to a first-half Lee Tomlin strike, it looked like a fairytale return.
But City goalkeeper Richard O'Donnell had not read the script and pulled off a superb save to leave the unfortunate target man still looking for his opening goal.
He only had to wait another seven minutes when he found himself in the right place at the right time to divert Jake Bidwell's header back across goal into the net from close range.
Bees head coach Dean Smith had hoped the penalty would open Hogan's account for the club and joked: "I spoke to my guys on the bench and said as he stepped up that at least the keeper wouldn't have seen him take one, but it was a great save.
"Scott is a natural striker and they know where to be when it matters. He's had a round of applause from the boys after the game because he's worked so hard for that, and has come back even stronger."
He added: "A re-rupture isn't nice at all so that goal was for him, his family and the medical team. He's a lot stronger player than I saw at Rochdale, he's a natural finisher and that's why the club went and got him. I certainly couldn't have afforded him at Walsall."
Hogan's injury time header cancelled out Tomlin's goal just before the break when he silenced the Griffin Park boo-boys with a crisp strike from the edge of the area that gave Bees keeper David Button no chance.