Cerci saw his last-gasp spot-kick saved by Fiorentina goalkeeper Antonio Rosati. The outcome handed the crucial sixth place to Parma and Cerci was understandably distraught after the miss.
"What has happened to Cerci is part of football," Toro coach Giampiero Ventura said to Gazzetta dello Sport. "I have seen players like (Roberto) Baggio and (Franco) Baresi cry for the same reason. But those who don't try don't make mistakes.
"You can miss penalties, it happens. But Alessio should be proud of his extraordinary season. He has scored 13 goals and set up a further 11."
Toro midfielder Jasmin Kurtic also offered some words of support for the Italy international.
"Cerci was crying his eyes out," Kurtic said. "But we cannot forget that it is thanks to him that we were able to get this far.
"No-one expected us to have a chance to qualify for Europe at the start of the season. Cerci is a very strong player, of high European level. I'm convinced he will have a great World Cup."
Cerci was one of three Toro players - along with Matteo Darmian and Ciro Immobile - named in Italy's preliminary World Cup squad earlier this month.
Despite Sunday's setback, which has seen Toro end the campaign in seventh spot, one point adrift of Parma, Ventura is satisfied with his side's season overall.
"I am very proud of my players and of what they have achieved," Ventura said. "It would have been fantastic to have qualified for Europe but we have shown an image of being a team that plays good football.
"Our performances have been rewarded with three Toro players being included in Italy's (preliminary World Cup) squad.
"It has been an important campaign in view of the future of this team. We cannot forget that three years ago we were tenth in Serie B and now we are disappointed to have just missed out on Europe.
"In any case, we have to congratulate Parma and their coach Roberto Donadoni as they too deserved to be in the Europa League qualifying round."