The pair scooped up three awards each at the 24th edition of the show, which celebrate achievement in the Latin music industry.
"It seems incredible to me that it changed the lives of so many others," said Karol G after winning album of the year.
It was the first time the ceremony was held outside the United States, taking place in Seville, Spain.
Shakira picked up song of the year and pop song of the year for Shakira: Bzrp Music Sessions, Vol. 53, with her collaboration on TQG with Karol G winning best urban/fusion performance.
The Colombian popstar dedicated her awards to her children, saying: "I have promised them I will be happy."
She also spoke about "tough moments", possibly referring to her split with footballer Gerard Pique and tax evasion charges in Spain. She denies evading millions of euros in tax between 2012 and 2014 and her trial is due to begin on Monday.
"I also want to share this with my Spanish audience, who has been there with me through the good and bad times.
"In those hard and tough moments I've experienced here in this country, I have loved so much but at no moment has stopped giving me love and support."
Fellow Colombian star Karol G said she was "happy to have some of those who teamed up" with her at the show.
"This is a very special album that changed my life," she added.
Spanish singer-songwriter Rosalia did not win anything but opened the show with a powerful performance paying tribute to the art of flamenco.
There was also a historical first with Laura Pausini being the only artist of non-Iberian heritage to receive the person of the year honour.
Fans were surprised at the lack of success for Puerto Rican artist Bad Bunny, who does feature on Coco Chanel by Eladio Carrion which won best rap/hip hop song.
But there was wider unhappiness over the decision to hold the awards in Seville, because of a multi-million pound deal with its regional government.
Some fans have criticised the ceremony for a lack of representation, saying a large number of awards have previously been wonby Spanish people.
One fan wrote on social media: "Bring back the Latin Grammys to Latin America."
You can find a full list of winners and nomineeshere.
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Shakira and Karol G were the two big winners at the annual Latin Grammys.