Massa was penalised by the stewards after being judged to have illegally crossed the white line of the pit entrance, which saw him drop from fourth place and subsequently see the Italian outfit narrowly lose out on second place in the constructors' championship to Mercedes.
However, Di Montezemolo branded the decision as "disproportionate and unjust".
He told RAI Television: "Every so often, the gentlemen who come to the races to act as stewards make decisions that are a bit ridiculous and anachronistic.
"One needs to be careful that we maintain credibility, for the work of the teams that invest money and for the drivers who risk their lives."
The Ferrari supremo was also critical of the steward's choice to penalise Lewis Hamilton over a collision with Williams driver Valtteri Bottas.