The Gunners' summer signing scored for just the second time since his £65million-move from Chelsea to put his side 1-0 up in the 89th minute at Brentford.
Havertz came on in the 79th minute to replace Gabriel Martinelli.
Just 10 minutes later, he was running towards the away end doing his trade mark celebration.
Bukayo Saka sent a brilliant, curling cross towards the far post, leaving Havertz to head it down past Brentford's Mark Flekken.
At the final whistle, Mikel Arteta - who was managing his 200th game for Arsenal on Saturday afternoon - embraced Havertz, before pushing him towards the away end with a huge grin on his face.
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The pair, and the rest of the Gunners stars, soaked in the praise from the away fans in the corner of the G-Tech Stadium who were singing Havertz's name and giving their side a standing ovation.
In truth, Arsenal had struggled to take their chances against Brentford, with the hosts themselves coming agonisingly close on numerous occasions.
Oleksandr Zinchenko made an incredible block in the closing stages of the game as he cleared Neal Maupay's off the line.
The Gunners have conceded the least goals in the league, letting in 10 since the start of the campaign.
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Returning goalkeeper Aaron Ramsdale was also praised by his teammates at full-time for keeping a cleansheet, with no.1 keeper David Raya unable to play due to being on loan from the Bees.
Arsenal will now finish the weekend at the summit of the top-flight - a point above the Citizens following their 1-1 draw against third place Liverpool.
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