The Androni Giocattoli-Venezuela rider swerved violently with the finish line in sight in the Danish town of Horsens causing Team Sky's Cavendish and race leader Taylor Phinney of BMC Racing to crash.
Ferrari angered many in the peloton by his initial refusal to accept blame for the incident and Cavendish was among several riders who took to Twitter to suggest his rival should be removed from the race by officials.
But in an apparent climb-down in the face of the criticism, Ferrari's team have now confirmed the rider will make a public apology before the fourth stage of the race.
"After getting over the nervous tension of the race, Roberto Ferrari has declared he will publicly apologise to Mark Cavendish and to the other riders involved in the fall at the end of stage three," a team statement read.
Cavendish suffered severe grazes to his thigh and a cut to his shoulder in the crash while Phinney sustained damage to his ankle. Both riders will, nevertheless, continue in the race.
William Bonnet and Mickael Delage of FDJ-BigMat were also injured in the pile-up.