In a statement on Friday, the Indonesian criticised Juventus for publicising details of the deal.
"Throughout Inter's long and storied history, the club has always stood for integrity and honesty, and we have made it our mission to uphold and continue that tradition," Thohir said.
"During the January transfer window, Inter has taken part in numerous private discussions to improve our club both on and off the pitch. Conducted in a professional manner these discussions should remain private, making public comment before the negotiations are final only hurts the process," he wrote.
Inter and Juve were all set for the swap when Inter fans wrote an angry open letter to the club and on Tuesday staged furious protests outside Inter's headquarters.
Inter then pulled out of the deal.
Juventus were enraged by Inter's actions and general manager Giuseppe Marotta called a news conference on Wednesday claiming his president Andrea Agnelli had received confirmation of the deal from Thohir via text message the previous day.
"The main reason we called this press conference was the lack of respect shown towards two serious, professional footballers," Marotta said.
"My being here is a necessary act to protect Juventus and the professionals who have been treated unfairly.
"It's the first time in over thirty years of dealing with players' transfers that I have been part of an unfortunate situation such as the one which has been created here."
Thohir has endured a difficult start since buying 70 percent of Inter and taking on all of its 180 million euro debt in November.
Since then Inter, joint fifth in Serie A ahead of Sunday's match at home to joint-bottom club Catania, have won only one of their last eight league matches.
Thohir has come under fire in recent weeks for telling fans that the club is in a transitional period.
"In everything I do, I believe there are core principles of success, including being hard-working, honest and reliable. I am committed to living out these principles with Inter and pushing the club to achieve at the highest level," added Thohir.
"As president of Inter it is my role to evaluate the performance of our personnel and challenge myself and our entire club to excel - management, players and staff.
"I cannot allow anyone outside our organisation to publicly critique our internal processes, and will defend Inter and what we stand for with everything I have.
"At Inter, we have always acted responsibly and in good faith, and will continue to make decisions that are in the best interest of the club both now and for the future."
(Editing by Patrick Johnston)
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