The pair are now self-isolating separately following the latest Government guidelines and will not be able to continue on the BBC 1 show.
The Russian professional dancer and Olympic boxer made history as part of the BBC show’s first same-sex pairing.
The rest of the cast are unaffected and the show will continue this Saturday night on BBC One.
A statement from the BBC said: "Nicola Adams and Katya Jones are to leave Strictly Come Dancing after Katya tested positive for Covid-19.
"Katya is asymptomatic and the pair are now self-isolating separately following the latest government guidelines. As part of the protocols outlined ahead of the series, this sadly means they will no longer be able to take part in the competition."
Adams said: “I’m absolutely devastated my Strictly journey has come to an end so soon. I had so much more to give and so many people to win this for.
"But I just want to say a huge thank you to Katya for being the best dance partner anyone could ask for.
“She pushed me way out of my comfort zone and it’s been an incredible experience. I’m gutted to be out of the competition but in these unprecedented times and as frustrating as it is, the Covid measures in place are to keep everyone safe, and I’m doing what I can to help.
"I’ll be spending the next 14 days isolating so I’d like to apologise in advance for the ridiculous amount of TikToks I’ll be posting, in my new found free time when I’m not gaming."
Adams and Jones performed a jive to 'Greased Lightnin'' from the musical Grease but judges scored them just 19 points putting them in the bottom two.
On Sunday, Adams wrote on Twitter: "Last night was a real wake up call but I’m glad me and katya made it through. I’m going to be working extra hard on the next dance routine because I really don’t want this journey to end."
Jones said: “Dancing with Nicola has been an absolute inspiration. She’s given her all each and every week and we were so excited to create more dances in the competition.
“Of course, I’m devastated to leave this way but I’ve made a friend for life and loved every moment of this special journey. I’d like to wish good luck to all the remaining couples.”
Sarah James, Strictly Come Dancing’s executive producer, said: “We are incredibly sad that these unfortunate circumstances mean that Nicola and Katya are unable to continue on Strictly.
“They are a brilliant partnership and had already achieved so much during their time on the show.
“We’d like to thank them for their commitment and although their time in the competition has sadly come to an end we are hopeful that there will be opportunities for them to dance again in the future.”