The Jets said he would not play in the evening's home-opener against the Anaheim Ducks.
Scheifele tested positive for the coronavirus Wednesday morning, but was asymptomatic.
He produced a negative test and would have been cleared to play Thursday had he produced another prior to puck drop.
But the Jets stated on the team's Twitter feed the forward will remain in COVID-19 protocol.
"We would have game-time decisions all the time," Jets head coach Paul Maurice said following his team's morning skate.
"The difference is if a guy's got a pulled groin, you don't have to worry about it spreading to the guy who sits beside him on the plane."
Scheifele is the second Winnipeg player to test positive for COVID-19 this week after captain Blake Wheeler was put in league protocol Monday with the team in Minnesota prepping to take on the Wild.
Wheeler, who was symptomatic after testing positive, and the Jets opened their season with games in Anaheim and San Jose, Calif., last week.
All of Winnipeg's players are vaccinated.
According to the NHL's rules for the 2021-22 season, Wheeler must isolate from the club for at least 10 days and will require a doctor's approval to return once he's symptom-free.
Scheifele and Wheeler make up two-thirds of Winnipeg's top line with Kyle Connor.
"We're not surprised by anything," Jets centre Paul Stastny said.
"The trainers gave us a warning that there might be a trickle down. So whether more guys go in protocol or not, I think we'll be ready for it. Not as nervous as what you would have been last year.
"It's unfortunate times right now, kind of unforeseen. But nothing comes easy in this world."
Jets defenceman Nate Schmidt tested positive for a second time with Vancouver last season when the Canucks had a massive outbreak that impacted 21 players and four coaches.
"This is going to be our reality across the league," he said. "It's part of what we have to deal with.
"(COVID-19) is such a ghost. You just never know, that's what makes it hard."
The Jets also restricted media access starting with Thursday's morning skate, which includes a ban on in-person availabilities until further notice.
Scheifele tied for second on the team with 21 goals during the NHL's pandemic-shortened 2020-21 campaign, and led Winnipeg with 63 points.
The 28-year-old from Kitchener, Ont., has two assists in two games this season after sitting out the Jets' opener as he served the final game of a suspension handed down during last spring's playoffs.
Winnipeg recalled forward Dominic Toninato from American Hockey League's Manitoba Moose in a corresponding move Thursday.