Following a goalless first leg in Belgium last week, the Hibees looked on course to make it to the main phase for the first time after second-half goals from Jason Kerr and Felix Passlack overturned a stunning first-half opener from teenage forward Josue Vergara.
But Christian Burgess equalised in the 84th minute before Hibs midfielder Chaiwa slid the ball into his own net in stoppage time, ensuring another agonising European exit after a 4-3 aggregate defeat by Legia Warsaw at the same stage a year earlier.
Boss David Gray made two enforced changes to the Hibs team that started in Belgium as injured pair Josh Campbell and Owen Elding were replaced by Jamie McGrath and Socceroo and club captain  Martin Boyle.
Gent arrived at Easter Road unbeaten in their seven matches this season and they started brightly, but at the other end Hibs captain Boyle had a shot on the turn deflected over before Josh Mulligan headed wide.
Boyle also released Nathan Lowe in the box but the on-loan Stoke forward blazed over.
The Socceroo, who was left out of Tony Popovic's eventual World Cup squad, had the ball in the net in the 47th minute but it was ruled out for handball.
Hibs' dream was killed off though when Chaiwa could only succeed in knocking the ball into the net from the edge of the six-yard box as he raced back to try to prevent Ibrahima Cisse getting on to El Hadji Seck's pass across the face of goal.
"It's really hard to put it into words, in terms of the feeling in the group," said Gray.
"It hurts, it's going to sting. It's hard to be critical of the players over the effort they've put in. I think over the two legs we deserved to go through."
Gray had only words of sympathy for Chaiwa after his late own goal.
"Miguel covered every blade of grass but in the last minute in his recovery he put it into his own net," said the manager.
"It's my job, the staff's job to get around the players. The big thing in these moments is we stick together, the big characters need to pick the other ones up. That's also my job and my staff's job."
7°C