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The singer shared the message on her website on Tuesday, alongside an image that showed their first public meeting at the Lion King premiere in London back in 2019.
"Thank you Meghan for your courage and leadership. We are all strengthened and inspired by you," she wrote.
On international women's day, Beyonce shared a post to her website acknowledging 12 women who she deemed to be 'rule breakers'.
Meghan was one of the women featured in the post, with Jane Fonda, and Democrat politicians Stacey Abrams, Maxine Waters and Alexandria Ocasio-Cortez also included.
Beyonce wrote: "For those who created their own way to tell their stories, found other avenues to get to the destinations, and broke every rule in the process, We See You! We salute each and every one of you on this International Women's Day."
Meghan and Beyonce share a mutual friend, Serena Williams, who reportedly helped the two meet.
According to Grazia, Meghan's introduction to Beyoncé "marked the culmination of a long process to orchestrate a meeting."
"Meghan had been a fan of the singer for years - she used to post tributes on her now-deleted Instagram account - and has long thought of her as a dream dinner guest,' the magazine reported wrote at the time.
Meghan and Prince Harry were interviewed by Oprah about their lives since they moved to California after giving up their royal duties for more privacy and safety.
She admitted that she was left feeling suicidal during her time as a royal and sought help after experiencing 'suicidal thoughts'.
"I just didn't see a solution," Meghan said candidly during the two hour TV chat, discussing the mental health toll of the vitriol that was thrown her way.
"Look, I was really ashamed to have to say [I was suicidal] at the time and ashamed to have to admit it to Harry especially, but I knew that if I didn't say that I would do it. I just didn't want to be alive anymore."
"It takes so much courage to admit you need help," she added, "to admit how dark of a place you're in."
When asked by Oprah just how close she got to taking her life, Meghan responded that her suicidal thoughts were "real and frightening", adding that at points she couldn't be left alone.
She harrowingly explained that when she asked if she could obtain mental health support she was told that she couldn't.
"I went to one of the most senior people to get help. I share this because there are so many people who are afraid to voice that they need help, and I know personally how hard it is to not just voice it, but when you voice it... [to hear someone say] no," Meghan said.
Meghan and Prince Harry claimed a member of the royal family commented on Archie's skin colour before he was born, questioning 'how dark' his skin might be when he's born.
"In those months when I was pregnant, all around the same time we have in tandem the conversation of he won't be given security, he won't be given a title, and also concerns and conversations about how dark his skin might be when he was born."
"Who was having that conversation with you? What?," asked a visibly shocked Oprah.
"So, um... there are several conversations about it with Harry," Meghan responded.
"About how dark your baby is going to be?," followed up Oprah.
"Potentially, and what that would mean or look like," she explained. "It was relayed to me from Harry. Those were conversations that family had with him [Harry]."
The interview was watched by over 17 million viewers in the US when it was shown on CBS. More than 12 million UK viewers tuned in for the broadcast on Monday evening.