The deal is subject to the player passing a medical and agreeing personal terms, the Portuguese champions said in a statement on Thursday before adding the fee could rise to 47 million euros depending on variable conditions.
Porto also said Atletico had agreed to sign Portugal midfielder Ruben Micael for five million euros.
Falcao, 25, grabbed 38 goals last season to help his team claim the Premier League-Portuguese Cup-Europa League treble.
He also became the record scorer in a UEFA club competition campaign with 17 goals in the Europa League.
The previous mark was held by German great Jurgen Klinsmann who netted 15 times when Bayern Munich lifted the 1996 UEFA Cup.
Falcao scored 73 goals in 84 games for Porto after joining the club in July 2009 from Argentina's River Plate for 5.5 million euros.
The striker, who last month extended his Porto contract until 2015, has won 31 caps for his country and scored nine international goals including two that helped Colombia reach the Copa America quarter-finals in July.
Atletico sold Argentina forward Sergio Aguero to Manchester City in July in a deal reported by British media to be worth about 45 million euros.
Micael, 24, joined Porto in January 2010 from domestic rivals Nacional Madeira.
He has become a regular in Paulo Bento's Portugal squad after scoring twice on his debut in a friendly against Finland in March.
