UEFA confirmed at their ExCo in Nyon on Wednesday that Atletico's 67,000-seater stadium has been chosen to host the showpiece match for next season's competition.
Atletico have made the final in two of the last four seasons, losing to Madrid on both occasions.
Estadio Metropolitano's first game was played on Saturday, with Atletico winning 1-0 at home to Malaga in La Liga.
A UEFA statement read: "Madrid's Estadio Metropolitano has been selected to host the 2019 UEFA Champions League final on 1 June of that year.
"Madrid will become only the second city to have held five or more European Cup finals after London, and the fourth to have hosted the event in separate stadiums after Amsterdam, Paris and Munich."
This season's tournament will culminate with the final in Kiev.
UEFA also revealed the 2019 Europa League final will be played in Baku's Olympic Stadium, after Azerbaijan missed out to Atletico's new home in the Champions League selection process.
Meanwhile, that year's Super Cup will be hosted in Besiktas' stadium.