Messi was introduced to the last-four match only as a second-half substitute by Valverde.
The Argentinian was nursing a minor leg injury sustained in the 2-2 La Liga draw against Valencia last weekend.
‘Leo is fine,’ Valverde is quoted as saying by Marca. ‘We prefer not to take risks at this time of the season.
‘He had some discomfort and we decided it was for the best.’
Malcolm, who deputised for Messi, impressed for the home side, netting Barcelona’s equaliser after 57 minutes.
But Valverde’s side must now score at least one goal at the Bernabeu to reach the final.
‘We have to score, so the tie is open,’ he added.