Massa will lose his Ferrari Formula 1 seat at the end of 2013 following eight seasons in the race team, interrupted only by his mid-'09 head injuries.
The Brazilian had been under Ferrari's wing since his junior career, and was placed at Sauber for 2002 and '04-05 alongside Ferrari testing duties.
Ferrari confirmed on Wednesday that it has brought its 2007-09 driver Kimi Raikkonen back into the fold to take Massa's place alongside Fernando Alonso.
Don't forget how good Massa was
"I wish to thank Felipe with all my heart and also on behalf of all our fans around the world, for the extraordinary job he has done for the team over so many years," said Domenicali.
"Felipe has always behaved like a real team player. Together we have lived through some great times and also a few dramatic moments, which have helped to cement a truly unique relationship on both a professional and personal level.
"He will always be part of our family and we wish him all the very best for the future.
"Now we must concentrate all our efforts on the remaining seven races of the season and we know that, as always, we can count on Felipe's contribution, while we work together to reach our goals."
Massa can walk out of Ferrari proud
Alonso added that it would be tough to say farewell to Massa.
"I want to thank Felipe for all the support he has given me and the team during this journey we have made together over all these years," said the Spaniard.
"Come the end of the season, it will not be easy to say goodbye to a team-mate like him.
"He has always been truly professional and loyal to the team and I am sure that right to the end, he will do his utmost for the Scuderia that he loves so much."