"I've told him that he was free to go and wasn't welcome at Toulon any more," he added.
Following Bougjellal's comments, Savea spent five weeks on the bench before being selected ahead of fellow former All Black Malakai Fekitoa.
Savea played the full 80-minute clash against Lyon but his performance was not noted by French media.
Instead, the side as a whole was criticised for its scrappy form.
With two more yellow cards issued, Toulon now hold the worst disciplinary record in the Top 14.
"It's the image of our whole season. We're always missing a little something," Toulon assistant coach Juan Martin Fernandez Lobbe told Agence France Press.
"We were shown two yellow cards, it's difficult to accept. We couldn't have won but we're not even taking a point home with us. It's frustrating."
Toulon are currently placed tenth in the Premiership with eight wins and 12 losses.
Last week, Savea voiced his support for the Muslim community in the wake of the Christchurch shootings.
Savea said he was "still heartbroken" over last Friday's two attacks on mosques that left 50 people dead and many injured.
"I've been privileged enough to learn about Islam through my wife's family, especially her grandparents," Savea tweeted.
"They've been to Mecca twice, they pray 5 times a day, they encouraged me to fast during Ramadan and taught me what it means to be a Muslim.
"And I will make sure my children learn about Islam too because it's a beautiful religion, and Muslims are the kindest people I have met. I am still so heartbroken over Friday's events and I want the Muslim community to know that I stand with you all."
