The Colombian international, who recently represented his country at the Copa America in Chile, was the Primeira Liga top goalscorer in each of the three seasons he spent at the Estádio do Dragão.
Martinez, 28, leaves Porto having won the Primeira Liga title in 2013 and the Supertaça Cândido de Oliveira in 2012 and 2013.
Diego Simeone’s side activated Martinez’s €35m release clause, and the striker admitted that he was on his way to the Spanish capital after Colombia were knocked out of the Copa America by Argentina.
“I can confirm I am going to Atletico,” said Martinez. “I am going there for four years, but I still don’t know when I will be introduced.”
But Martinez’s agent, Luis Henrique Pompeu, claimed he was shown a lack of respect by Porto president Pinto da Costa.
Pompeu said: “I sent a fax with a formal offer of €35m to activate the buy-out clause for Jackson Martinez, as clearly stipulated last year.
“It was a surprise to me that the Porto president would not meet me. I demand some respect and want him to fulfil what has been agreed.”
Martinez, who had also been linked with a move to AC Milan and Arsenal, scored 92 goals in 132 appearances in all competitions for Porto, with his final season in the north of Portugal being his most successful in front of goal. The Colombian scored an impressive 32 goals in 41 appearances in all competitions during the 2014/15 campaign.
FC Porto have sold more players for over 28m than any other club in world football and Martinez’s move means the club has now received almost €700m in transfer fees since Porto won the Champions League under José Mourinho in 2004.
Arsenal, Barcelona, Chelsea, Lazio and Real Madrid are FC Porto’s closest challengers having sold five players for more than €28m. Benfica, meanwhile, have sold four players for over that amount.
Martinez follows Ricardo Carvalho (€31m), Anderson (€31m), Pepe (€31m), Radamel Falcao (€39.2m), Hulk (€54.6m), James Rodriguez (€44.8m), Eliaquim Mangala (€58.8m) and Danilo (€32m) out of the club.
Four of the nine players to leave the Estádio do Dragão for a significant sum have moved to Madrid. Martinez follows Falcao to Atletico while Danilo joins Pepe this summer at Real.
Real Madrid have bought 18 players for over €28m, making them the team to buy the most players for over that amount.
Manchester United are the biggest spending English side with 13 big-money signings.
Nani moved from Sporting to Old Trafford for €25m in 2007 and the Portugal international, 28, has joined Fenerbahce this week. The winger, who returned to Sporting on loan last season, was told by United boss Louis van Gaal that he was surplus to requirements.
Fenerbahce moved quickly to sign Nani for a fee of €6m, and now the winger will be hoping to impress ahead of next summer’s European Championships in France.
During his time at Old Trafford, Nani won four Premier League titles, four Community Shields, the League Cup, UEFA Champions League and FIFA Club World Cup. The Portugal international also scored 40 goals in 230 appearances for the Red Devils.
During his loan spell with Sporting last term, Nani scored 12 goals in 35 appearances in all competitions. He also scored in Sporting’s penalty shoot out win over SC Braga in the Taça de Portugal Final, which earned Sporting their first trophy since 2008.