The 53-year-old was in interim charge at the Mestalla ever since Gary Neville was sacked in late March.
Having guided the club away from relegation danger, Ayestaran has now been rewarded with a two-year contract.
However, in the official statement, there was no word on Phil Neville's future at the club.
The Englishman, who has coached Los Che since last summer, recently revealed that he hoped to retain his job.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| 1 | Barcelona | 14 | 11 | 1 | 2 | 42 | 14 | 28 | 34 |
| 2 | Real Madrid | 13 | 9 | 3 | 1 | 28 | 11 | 17 | 30 |
| 3 | Atletico MadridAtletico | 14 | 8 | 5 | 1 | 21 | 8 | 13 | 29 |
| 4 | Villarreal | 13 | 7 | 4 | 2 | 25 | 21 | 4 | 25 |
| 5 | Athletic Bilbao | 14 | 6 | 5 | 3 | 20 | 13 | 7 | 23 |
| 6 | Osasuna | 14 | 6 | 4 | 4 | 19 | 22 | -3 | 22 |
| 7 | GironaGirona | 14 | 6 | 3 | 5 | 20 | 18 | 2 | 21 |
| 8 | Mallorca | 14 | 6 | 3 | 5 | 13 | 12 | 1 | 21 |
| 9 | Real BetisBetis | 14 | 5 | 5 | 4 | 16 | 16 | 0 | 20 |
| 10 | Real Sociedad | 14 | 5 | 3 | 6 | 11 | 11 | 0 | 18 |
| 11 | Celta Vigo | 14 | 5 | 3 | 6 | 22 | 24 | -2 | 18 |
| 12 | Sevilla | 14 | 5 | 3 | 6 | 13 | 18 | -5 | 18 |
| 13 | Rayo Vallecano | 13 | 4 | 4 | 5 | 13 | 14 | -1 | 16 |
| 14 | Leganes | 14 | 3 | 5 | 6 | 13 | 19 | -6 | 14 |
| 15 | Getafe | 14 | 2 | 7 | 5 | 10 | 11 | -1 | 13 |
| 16 | AlavesAlaves | 14 | 4 | 1 | 9 | 15 | 24 | -9 | 13 |
| 17 | Las PalmasLas Palmas | 14 | 3 | 3 | 8 | 18 | 25 | -7 | 12 |
| 18 | Valencia | 12 | 2 | 4 | 6 | 12 | 19 | -7 | 10 |
| 19 | Espanyol | 13 | 3 | 1 | 9 | 12 | 26 | -14 | 10 |
| 20 | Real ValladolidValladolid | 14 | 2 | 3 | 9 | 10 | 27 | -17 | 9 |
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