He could hardly have made a more impressive comeback, showing his colleagues how to finish after Leeds, currently eighth in the Championship, held out stubbornly until the 79th minute, 11 minutes after Henry had come on to a rapturous welcome from the home fans.
It was his 227th Gunners goal and Arsenal's reward is a fourth round tie at home to Aston Villa.
'It's kind of weird, I only came back from holiday in Mexico 15 days ago, I never thought I was going to be playing for Arsenal again and then score the winner,' he told ESPN.
'The feeling I had when I scored was amazing, I've rejoined the club as a fan, I just wanted to come and help the team, and then I end up as man of the match - it wasn't my plan to be a hero. I'll always remember tonight. When it comes to Arsenal, something happens to me.'
The 1998 World Cup winner settled a game that was a repeat of the draw for the same round last season, which saw Leeds come within a handful of seconds from winning at the Emirates Stadium but went on to lose in the replay.
Arsene Wenger had allowed captain and top scorer Robin van Persie to take a holiday, with Marouane Chamakh taking his place up front before departing for the Africa Cup of Nations.
Otherwise it was close to being as strong a starting line-up as a series of injuries to defenders would allow, with Wojciech Szczesny, Aaron Ramsey, Alex Song, captain for the night Mikel Arteta and Andrey Arshavin all included.
Henry, as expected, began on the bench, as did Theo Walcott, the inheritor of the number 14 shirt the Frenchman left behind four-and-a-half years ago when he decamped to Barcelona.