Henry took a pass from Alex Song in his stride in the area before steering a composed, angled, right-footed finish tantalisingly out of the reach of Leeds United keeper Andy Lonergan.
It finally broke the stubborn resistance of Leeds and was the signal for an outpouring of emotion as Henry pumped his chest in celebration after racing to hug his mentor Arsene Wenger on the touchline.
Arsenal keeper Wojciech Szczesny raced the length of the field to join the celebrations while Henry later indulged in a spot of impromptu cheerleading as he urged the supporters who worship him to even greater backing for Arsenal in the closing stages.
It was the perfectly scripted finale to a contest that needed Henry's Midas touch against a Leeds side who battled in a manner that did manager Simon Grayson and their magnificent travelling support great credit.
At the final whistle, with the first task of his temporary return to the club completed, Henry raised his arms to the heavens before falling into the arms of his Arsenal colleagues and taking the acclaim of an elated crowd.
Henry's presence, even on the bench, enlivened the stadium when he came out to warm up and later when his name was announced to rapturous applause.
And the 45 minutes that followed only increased the appetite and anticipation for his return as Arsenal dominated but failed to breach a resilient and well-organised Leeds defence.
With leading scorer and captain Robin van Persie rested, attacking duties fell to Andrey Arshavin and Marouane Chamakh, the pair combining in the opening moments only for the Russian to fire wildly over the top.
Sebastien Squillaci then headed narrowly wide and Aaron Ramsey was unable to navigate a way around Lonergan after he was played into the area by Arshavin.
Leeds United's big chance, in a half they spent mainly on the retreat, came when Luciano Becchio found space in the box but shot wastefully off target.
Arsenal's defensive resources have thinned out in the face of mounting injuries - and they were depleted further before the interval when Francis Coquelin pulled up with a hamstring problem and was replaced by Nico Yennaris.
The momentum remained with Arsenal after the break as Lonergan saved well low to his left from Mikel Arteta after the Spaniard was set up by Chamakh, and Arshavin fired across the face of goal after picking up Zac Thompson's misplaced pass.
Henry's increasingly energetic sprinting along the touchline drew a loud reaction from Arsenal's fans and he was finally introduced with 22 minutes left, replacing Chamakh. Theo Walcott also came on for Alex Oxlade-Chamberlain.
Henry was given a hero's welcome as he set about the business of attempting to break down a Leeds side proving as stubborn as they had been here at the same stage of the FA Cup last season.
And the moment Arsenal had been waiting for came with 12 minutes left as Henry gathered Song's pass in his stride before sparking scenes of ecstasy on and off the pitch with a perfect finish to set up a fourth-round tie at home against Aston Villa.
Leeds refused to be distracted by the euphoria and almost snatched a replay in the closing stages as Szczesny saved well from substitute Mikael Forssell.
This, however, was Henry's night and Henry's story. Now Arsenal fans will hope he can write fresh chapters before returning to the United States.
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