Argentina edged past Louis van Gaal's Netherlands in a tense penalty shootout, on their way to claiming World Cup glory in December.
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Weghorst scored twice in the final seven minutes to take the tie to extra time after a Messi penalty had given the South Americans a two-goal cushion.
Tensions boiled over between the two sets of players as the game entered its final stages and the usually reserved Messi even found himself embroiled in the unsavoury scenes.
Speaking at his first media outing since lifting the World Cup, the Argentine admits he regretted his outburst aimed at the Manchester United striker.
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After seeing Weghorst in eyeshot, Messi interrupted his own post-match interview and shouted: "Qué miras bobo? Andá para allá" - translated to 'what are you looking at, idiot? Go over there.'
The video clip immediately went viral but for Messi, there is a feeling of shame around his actions towards the Dutchman.
When asked about the footage Messi replied: "I don't like this picture.
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"I don't like what I did. There was a lot of tension and it came out naturally. A lot had happened with this player and two others during the match. It came out naturally. I don't like this image."
But the Paris Saint-Germain forward will find it difficult to shrug off the comments as jubilant fans in his homeland have hijacked the phrase.
T-shirts, mugs and caps are readily seen in the Argentine capital donning the famous words, leaving Messi unable to move on from the episode.
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After a two-week celebratory break, Messi returned to the French capital to resume duties at club level.
At 35 years old, this season could prove to be his most successful should he guide PSG to Champions League glory in June.
Messi is set to lead his troops into battle against Bayern Munich in two weeks as they hope to topple one of the favourites to lift the trophy in Istanbul.
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There is still no indication on whether Messi will extend his stay in Paris beyond this season despite reports suggesting he has a verbal agreement with the French champions for a 12-month extension.
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