"(Grimaldo) has signed for our club until June 30, 2030," said Atletico in a statement.
"A versatile left-back who can also play as a wing-back, central midfielder and even attacking midfielder, he stands out for his technique and vision."
The 30-year-old, who spent time at Barcelona's academy before joining Benfica in 2016, is currently at the World Cup with Spain.
Grimaldo moved to Leverkusen in 2023 and was a key part of their Bundesliga-winning side in 2024 under Xabi Alonso.
The attacking full-back is a set-piece specialist, netting six free-kicks over the last three seasons, and no player has more in that period in Europe's top five leagues.
Atletico had been linked with Marc Cucurella, who signed for rivals Real Madrid earlier in June, before moving for Grimaldo to bolster coach Diego Simeone's options.
The Rojiblancos finished fourth in LaLiga last season, 25 points behind champions Barcelona, and were beaten by Real Sociedad in the Copa del Rey final.