Taylor had 26 carries for 223 yards, also fumbling once. He started in place of sophomore Bradrick Shaw, who suffered a right leg injury last week against Utah State.
"When we recruited him and getting to know him, he is mature," said Badgers coach Paul Chryst. "He's a person with great focus and wants to take full advantage of this opportunity. I was proud of the way he was after the fumble and his response. He will learn from it and grow.
"Jonathan certainly has talent and he's gotten himself off to a good start, but there's a long way to go."
Badgers sophomore quarterback Alex Hornibrook completed 16 of 28 passes for 201 yards, with one touchdown and one interception.
The Badgers (2-0) got on the scoreboard first as Taylor broke free from an Owls defender and slipped between two others for a 64-yard touchdown at the 10:00 mark of the first quarter.
It didn't take long for Taylor to find the end zone again, breaking three tackles en route to a 29-yard score that gave Wisconsin a 14-0 lead with 6:40 to go in the first quarter.
Taylor surpassed his 87-yard, one-touchdown performance in Wisconsin's 51-19 win over Utah -- in the first half. He had 17 carries for 148 yards and two scores in the opening 30 minutes against FAU.
"Out of all the freshmen, it seems like he's the most ready," said Wisconsin junior left guard Micah Kapoi.
"He's in the film room a lot and he just gets it. The freshman class is coming along, but I think he's an early bloomer. He got it early and it shows. That's why Coach trusted him with starting and getting all those snaps."
The Owls (0-2) were stout on defense at certain junctures, including keeping the Badgers from extending their lead during a second-and-goal situation from the 2-yard line early in the second quarter. Taylor failed three times to get into the end zone. Sophomore linebacker Hosea Barnwell and junior safety Andrew Soroh stopped Taylor on the final try.
Junior safety Jalen Young led FAU with 14 tackles, including one for loss.
"We pride ourselves on being dominant and not letting them in our end zone," Young said. "When it comes to red zone defense we stood tall. Our confidence never wavered. We always had that confidence. We played fundamentally sound and did all the basic stuff and that's why we did what we did."
Hornibrook's interception came in the second quarter when he failed to see defensive end Leighton McCarthy, who returned the pick 15 yards to set up a 27-yard scoring drive that cut Wisconsin's lead to 21-14. The drive was capped by a 1-yard run by running back Devin Singletary with 4:29 left in the half.
The Owls failed to take advantage of Taylor's third-quarter fumble, recovered by FAU at its 36 while trailing 24-14. The Owls did hold the Badgers to just seven second-half points.
"We've got a lot of coaches who have been in big stadiums and big games, so I think that helps," said first-year FAU coach Lane Kiffin. "We don't get rattled and then all of a sudden assume it's going to be one of those big (blowout) games that happens in this situation sometimes.
"At the end of the day, our players have to make the plays and they did at times to make it a competitive game. I'm proud of the way those guys played. I just feel really bad for them because this really should've been a game right down to the wire, that could've gone either way."
FAU quarterback Daniel Parr completed 9 of 19 passes for 142 yards and one touchdown. DeAndre McNeal led the Owls in receiving with three catches for 103 yards, while Singletary paced the ground game with 17 carries for 68 yards and one score.
Wisconsin held the Owls to 248 yards, including 106 rushing yards. Penalties also hampered Florida Atlantic, which racked up eight for 73 yards.