Dantonio, who suffered a mild heart attack Sept. 19 and underwent surgery, had been planning to watch the game from the booth after returning to work Sunday.
But doctors discovered the blood clot during a routine post-operative examination and Dantonio was readmitted Thursday to Sparrow Hospital in Lansing, Mich.
Dantonio told ESPN's Quint Kessenich on Saturday morning that he had swelling and discomfort in his leg after Wednesday's practice and alerted the team Friday afternoon that he would not attend the game.
The 54-year-old Dantonio also missed the No. 24 Spartans win over Northern Colorado on Sept. 25, watching from home as as offensive coordinator Don Treadwell coached.
Dantonio told Kessenich he has the utmost confidence in Treadwell to "take the wheel" and "will not interfere" during the game. Dantonio's wife planned to be at the game chaperoning recruits.
Treadwell was coy when asked after the game if the coaching staff had any contact with him during the game.
"I don't know how much that I had, but I think at times some of the assistants would have potentially had some contact with him," Treadwell said. "He was involved as much as he could be, absolutely."
"I have never been on the phone so much during a game," defensive coordinator Pat Narduzzi quipped. "He was with us the entire time."
Dantonio's release date from the hospital has not been determined.
"I'm all good," Dantonio told Kessenich. "I'll be home soon."
"Blood clots are not uncommon following a number of surgical procedures and can occur after a cardiac catheterization procedure," said Dr. Chris D'Haem, Dantonio's cardiologist. "The clot can block blood flow and cause swelling and pain."
Dantonio attended his weekly news conference Tuesday and said that he'll be easing back into his routine but would follow doctor's orders.
"Coach Dantonio is doing well and his prognosis is excellent," Michigan State athletic director Mark Hollis said in a statement. "He was admitted to Sparrow Hospital for monitoring and treatment. The cardiologist told Coach D that it was in his best interest to sit out another game and to stay off his feet.
"Although Coach D will be unable to watch today's game from the press box, make no mistake that he remains in control of our football program. He was able to attend meetings and practices earlier this week, and since his hospitalization, he has been in regular contact with his coaching staff as well as the team captains and other team leaders."
Michigan State plays in-state rival Michigan, which is also unbeaten, next.
Adam Rittenberg covers Big Ten football for ESPN.com. He can be reached at firstname.lastname@example.org. Information from The Associated Press contributed to this story.