Veteran centre-back Felipe, 30, will join Atletico from the Portuguese giant in a €20million deal.
Felipe – who arrived from Corinthians in 2016 and made 93 Primeira Liga appearances in three years – is set to replace outgoing captain Diego Godin.
A league winner with Porto in 2017-2018, Felipe confirmed his exit from Estadio do Dragao.
"It was three years of living intensely blue and white with a new family that I built, and that will be remembered for the rest of my life!," Felipe wrote via his official Instagram account. "I just have to thank all the staff of the club, the board, the president, the coaches and team-mates with whom I lived in this period.
"I have a great affection for all the fans who are here and those who wait for hours at the door of the training ground or stadium. My thanks for the recognition and for everything you do for me!
"Porto made me feel at home and live great emotions, with achievements, goals, the Champions League, a lot of overcoming and delivering on the field.
"It became the club that I represented the most in my professional career and I was able to return to be called to the Brazilian national team and debut representing my country. There are no words to describe how much I have learned and evolved as a person.
"I wish the best of luck in the future for those who stay. I'll be in the crowd and I'll be forever grateful! Thank you!"