Weber's early seasons at Illinois indicated years of success to come with runs to the Sweet 16 in 2004 and NCAA tournament championship game in 2005, but since then the program saw a decline that Thomas thought was irreversible under Weber.
It's clear Thomas is ambitious to change the face of Illinois athletics.
Weber followed out the door behind football coach Ron Zook and women's basketball coach Jolette Law as changes Thomas has made since becoming athletic director in August.
Weber will be paid a buyout of $3.9 million (made up of payments of $1.3 million over three years). Combined with Zook and Law, Illinois will owe the coaches more than $7.1 million in buyouts.
That will not affect how much the school can pay the next coach, Thomas said.
"I'm confident we'll be competitive as we move forward," he said. "Those buyouts are paid with Division of Intercollegiate Athletics money. Those are moneys that come out of our budget. We're not receiving any type of institutional aid."
The Illini have missed the NCAA tournament three of the last four seasons, including this year, and have won only two tournament games since 2005.
They raised expectations this season with a 15-3 start and Top-25 ranking despite a young roster. But things quickly unraveled after Illinois beat No. 5 Ohio State on Jan. 10 as the Illini stumbled in12 of their last 14 games and exited from the Big Ten tournament in the first round with a loss to Iowa on Thursday.
"This is a bottom-line business and we all know it," Weber said Friday. "It's the reality of the coaching profession. I leave here with no regret. I leave this program on solid footing and (it) once again will experience the levels of success we enjoyed much of my time here."
During a tearful goodbye, Weber's wife and two of his three daughters stood by his side along with nine players and his coaching staff. He reminisced about the program's glory days in his first two seasons, reflecting on the thrilling overtime victory in Arizona to make the Final Four and watching from his hotel rooftop in St. Louis as Illini fans filled the streets in celebration.
Critics, however, pointed out that Weber won with players previous coach Bill Self had recruited and he never achieved the same success with his own players.
"I'm very proud of what this basketball program has accomplished during my tenure," Weber said.
Thomas bypassed associate head coach Wayne McClain to name assistant coach Jerrance Howard as the interim coach. Howard would like to stay on the future staff, Thomas said.
The Illini will play in the NIT if they receive an invitation Sunday night, but they will not accept an invitation to play in any other postseason tournament.
Illinois will begin a national search immediately and Thomas said he likely will use a search firm.
"There's going to be a lot of interest in this job," Thomas said. "We will move quickly but we will move diligently."