Brady said last week he was fighting a cold but did not miss a practice and played every snap of Saturday's divisional playoff victory over the Indianapolis Colts.
The Patriots also listed Brady as having a shoulder injury, a designation that has been relatively typical for the star quarterback.
Wednesday's session was the first of three practices the Patriots will hold this week. In Brady's absence, backup Ryan Mallett handled the roles of both first-team and scout-team quarterback, essentially filling both Brady's and Manning's shoes.
"It was fun," Mallett said of taking first-team reps. "It was a lot of fun. I like getting to play in our offense."
Mallett, who said he found out Brady would be absent early Wednesday, would not discuss why the two-time Super Bowl MVP wasn't present.
"You'd have to ask Coach," he said of Brady's absence. "I'm just doing what I'm told, doing my job."
Asked about Brady in his news conference, Bill Belichick would only say the team would release its first injury report later Wednesday.
In a lighthearted moment, Belichick, asked when the last time Brady surprised him was, replied, "This morning."
What was it that surprised him?
"We'll keep that between Tom and I," Belichick said.
Long snapper Danny Aiken was also missing from practice with an illness. The Patriots, who canceled Brady's scheduled news conference Wednesday, had additional hand-sanitizing stations set up in the locker room.
Meanwhile, the Patriots did have punter Ryan Allen, who left Saturday's game with a shoulder injury, on the practice field. Allen suffered an AC sprain, according to sources, and the team is hopeful he can rehab the injury this week to a point that he is good to go on Sunday.
Wide receiver Aaron Dobson, who was injured in Week 17 and had not practiced since then, returned to practice as he continues to work through a foot injury.
ESPNBoston.com's Mike Reiss and Field Yates contributed to this report.