The defender appeared to step on the Argentine's hand during Madrid's 2-1 defeat in the first leg of the Copa del Rey quarter-final at the Santiago Bernabeu.
Pepe has since apologised to Messi, claiming that it was an accident.
"I haven't seen it, but obviously if it is deliberate he will be punished," said Mourinho.
The second leg takes place at the Nou Camp next week.
Restore Data
| Team | P | W | D | L | F | A | GD | PTS | |
| C | Real Madrid | 37 | 29 | 7 | 1 | 87 | 26 | 61 | 94 |
| 2 | Barcelona | 37 | 25 | 7 | 5 | 77 | 43 | 34 | 82 |
| 3 | GironaGirona | 37 | 24 | 6 | 7 | 78 | 46 | 32 | 78 |
| 4 | Atletico MadridAtletico | 37 | 23 | 4 | 10 | 68 | 43 | 25 | 73 |
| 5 | Athletic Bilbao | 37 | 18 | 11 | 8 | 60 | 37 | 23 | 65 |
| 6 | Real Sociedad | 37 | 16 | 12 | 9 | 51 | 37 | 14 | 60 |
| 7 | Real BetisBetis | 37 | 14 | 14 | 9 | 48 | 45 | 3 | 56 |
| 8 | Villarreal | 37 | 14 | 10 | 13 | 64 | 64 | 0 | 52 |
| 9 | Valencia | 37 | 13 | 9 | 15 | 38 | 43 | -5 | 48 |
| 10 | AlavesAlaves | 37 | 12 | 9 | 16 | 35 | 45 | -10 | 45 |
| 11 | Osasuna | 37 | 12 | 8 | 17 | 44 | 55 | -11 | 44 |
| 12 | Getafe | 37 | 10 | 13 | 14 | 41 | 52 | -11 | 43 |
| 13 | Sevilla | 37 | 10 | 11 | 16 | 47 | 52 | -5 | 41 |
| 14 | Celta Vigo | 37 | 10 | 10 | 17 | 44 | 55 | -11 | 40 |
| 15 | Las PalmasLas Palmas | 37 | 10 | 9 | 18 | 32 | 46 | -14 | 39 |
| 16 | Rayo Vallecano | 37 | 8 | 14 | 15 | 29 | 47 | -18 | 38 |
| 17 | Mallorca | 37 | 7 | 16 | 14 | 31 | 43 | -12 | 37 |
| 18 | CadizCadiz | 37 | 6 | 15 | 16 | 25 | 49 | -24 | 33 |
| R | Granada | 37 | 4 | 9 | 24 | 38 | 72 | -34 | 21 |
| R | Almeria | 37 | 2 | 12 | 23 | 37 | 74 | -37 | 18 |
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