Franklin achieved the feat with his fourth goal in Friday night's blockbuster game against Geelong as spectators ran onto the SCG turf in the final quarter.
The 35-year-old joins Tony Lockett (1360 goals), Gordon Coventry (1299), Jason Dunstall (1254), Doug Wade (1057) and Gary Ablett senior (1031) in the exclusive club.
The SCG became a sea of red-and-white as thousands of spectators streamed onto the field, even before Franklin's shot had gone through the goals.
He was mobbed by teammates and supporters as the Foo Fighters' classic 'My Hero' played over the speakers.
Franklin eventually attempted to leave the field, with play to be stopped for at least 20 minutes so the crowd can be cleared off the arena.
Franklin started the match with 996 goals to his name, but he edged closer to the mark by nailing a set-shot from the pocket just before quarter-time.
He had a quiet second term before being handed a soft free kick midway through the third quarter that he converted from about 20m out.
Franklin's third was a powerful kick from 50m out directly in front, raising his hands in delight to the crowd after the ball sailed through.
The 1000th goal came late in the last quarter as he put through a set shot after being set-up by young gun Chad Warner.
Geelong young gun Jack Henry, who is seven centimetres shorter than Franklin, had the job on the Swans hero for most of the night.
He is in the final season of his mega nine-year, $10 million deal with Sydney, and Franklin has left the door open to play on in 2023.
That would give Franklin the perfect opportunity to overtake both Ablett and Wade to become the fourth most prolific goalkicker in VFL/AFL history.
Franklin kicked 580 goals in 182 games with Hawthorn between 2005 and 2013 before adding 420 more with the Swans since 2014.
Franklin was at the centre of the AFL's last crowd invasion back in 2008 when he kicked his 100th goal of the season in the Hawks' final home-and-away match.
Four-time Hawthorn premiership coach Alastair Clarkson, who left the Hawks last year after 17 seasons in charge, was at the SCG to watch his former star and was even spotted wearing a Swans scarf.
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