The 22-year-old joined Diego Simeone's side two years ago, but he has twice been sent out on loan to Real Betis and Rayo Vallecano.
Villarreal have the option to sign Baptistao permanently if the Brazilian proves to be a success at El Madrigal.
The deal is the second between the clubs this week, following Luciano Vietto's move to Atletico from the Yellow Submarine.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| 1 | Real Madrid | 31 | 24 | 6 | 1 | 67 | 20 | 47 | 78 |
| 2 | Barcelona | 31 | 21 | 7 | 3 | 62 | 34 | 28 | 70 |
| 3 | GironaGirona | 31 | 20 | 5 | 6 | 63 | 39 | 24 | 65 |
| 4 | Atletico MadridAtletico | 31 | 19 | 4 | 8 | 59 | 36 | 23 | 61 |
| 5 | Athletic Bilbao | 31 | 16 | 9 | 6 | 51 | 29 | 22 | 57 |
| 6 | Real Sociedad | 31 | 13 | 11 | 7 | 45 | 33 | 12 | 50 |
| 7 | Valencia | 31 | 13 | 8 | 10 | 34 | 32 | 2 | 47 |
| 8 | Real BetisBetis | 31 | 11 | 12 | 8 | 38 | 37 | 1 | 45 |
| 9 | Villarreal | 31 | 10 | 9 | 12 | 49 | 54 | -5 | 39 |
| 10 | Getafe | 31 | 9 | 12 | 10 | 37 | 43 | -6 | 39 |
| 11 | Osasuna | 31 | 11 | 6 | 14 | 36 | 44 | -8 | 39 |
| 12 | Las PalmasLas Palmas | 31 | 10 | 7 | 14 | 29 | 35 | -6 | 37 |
| 13 | Sevilla | 31 | 8 | 10 | 13 | 39 | 44 | -5 | 34 |
| 14 | AlavesAlaves | 31 | 8 | 8 | 15 | 26 | 38 | -12 | 32 |
| 15 | Mallorca | 31 | 6 | 13 | 12 | 25 | 36 | -11 | 31 |
| 16 | Rayo Vallecano | 31 | 6 | 13 | 12 | 25 | 38 | -13 | 31 |
| 17 | Celta Vigo | 31 | 6 | 10 | 15 | 33 | 46 | -13 | 28 |
| 18 | CadizCadiz | 31 | 4 | 13 | 14 | 21 | 41 | -20 | 25 |
| 19 | Granada | 31 | 3 | 8 | 20 | 32 | 60 | -28 | 17 |
| 20 | Almeria | 31 | 1 | 11 | 19 | 30 | 62 | -32 | 14 |
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