Rodriguez will join the Europa League winners on a four-year deal subject to a medical and will sign his contract after Uruguay's World Cup 2014 qualifiers against Venezuela and Peru next month, Atletico said on their website (www.clubatleticodemadrid.com).
The 26-year-old, who has 47 caps for Uruguay and an Italian passport, has been at Porto for four seasons and previously played for Benfica and Paris St Germain. He is known as "the onion" because of his reputation for making defenders cry.
"He is a very quick player, attacking and with a lot of character, a winner," Atletico sporting director Jose Luis Perez Caminero said.
"He will give us a lot of options in attack because he is multi-purpose and can play on either wing, whether taking defenders on or cutting inside onto his other foot."