The pair met in a clash between Barcelona and Levante in 2007, with Messi three years into his incredible career with Barca that saw him go on to score a whopping 672 times in 778 games.
Barca had a solid lead at the top of LaLiga over rivals Real Madrid, but saw their form slip in the run-in, allowing Los Blancos to overtake them and take back the title.
But before Frank Rijkaard's Barca threw away their place at the top of the table, one game they did manage to secure all three points in was against Levante.
Spanish FA president Rubiales is currently facing serious backlash for kissing Spain women's Jenni Hermoso on the lips during the World Cup trophy ceremony.
Now, fans have dug up a video of the controversial figure facing LaLiga legend Messi during his playing career - and let's just say he had a tough time against one of the world's best ever wingers.
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Playing at left-back, the footage shows Rubiales having to deal with a 19-year-old Messi on the right flank.
The first clip shows the Argentine fooling him into thinking he'd stopped to change direction, only to pass the ball round Rubiales and run past him, leaving the Spanish FA chief spinning in circles.
Messi ran Rubiales ragged, and Barca went on to win 1-0, with Samuel Eto'o scoring the only goal. Rubiales also picked up a yellow card during the game.
"Viva Messi," one fan wrote under the reposted footage.
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"Fine footage," another said.
Rubiales' mother has now ended her hunger strike after shutting herself into a church in Spain in defence of her son in a surprising twist in a saga that has seen the former footballer suspended from his role for 90 days by FIFA.
Rubiales insisted in a speech in a general assembly that he would not resign following the incident with Hermoso, which was broadcast live on TV round the world, despite the press being briefed he would step down.
FIFA have also banned the Spanish FA from contacting Hermoso, who also released a statement denying Rubiales' claims that the kiss was consensual.
Chelsea women's boss Emma Hayes has told talkSPORT that the kiss is just one example of a wider issue with the culture inside the Spanish FA, though, as she slammed the body for 'embarrassing' treatment of their players.
"Unless you've been in that position where things like that happen that are shocking, an assault that feels quite shocking, it's no surprise paralysis happens," she told talkSPORT's Hawksbee and Jacobs.
"You could see it happening with her in that moment, it was so odd and so weird. But when you become so accustomed to just going along with something, because nobody is listening, you don't react, you don't respond.
"Forget the kiss, he was picking players up, putting them over his shoulders. But this isn't just about that, this is years of players having to go on away trips, having to leave their doors open, perhaps going on trips where they were put in isolation.
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"They didn't get to socialise out of their camps. This is control. That's for me what's maybe being misunderstood in all of this. This isn't just about an isolated incident, it's years and years and years. You only have to see across Spain, the demonstrations and ramifications for the Spanish Football Association.
"This is an embarrassment for them and hopefully there will be some change because of it."