Jordan Taylor made two three-pointers around a pair of Keith Appling free throws to cut No. 18 Wisconsin's deficit to three late in overtime.
Draymond Green was sent to the line with 10.2 seconds left and a chance to ice the game for 10th-ranked Michigan State, but the senior forward missed both shots.
After Taylor missed a three, Ryan Evans pulled down the rebound and raced behind the three-point line before banking the ball off the backboard and into the net to send the crowd into a frenzy.
But the refs went the to replay to see if Evans got the shot off before time expired. According to the clock above the basket, Evans failed to get the shot off before the red light came on. However, the scoreboard clock was different and showed that Evans beat the buzzer.
The refs decided to call off the basket, giving Michigan State its 14th straight victory.
"We did. But, by rule we have to go by the clock that is on the backboard," referee Pat Driscoll said. "I don't know why there would be different (times) - it could be satellite, electronic, whatever - but by rule we have to go by the clock that is attached to the backboard. In our review on the monitor, the clock clearly showed zeros while the ball remained in the Wisconsin player's hands."
Green ended with 18 points and 14 rebounds for the Spartans (14-2, 3-0 Big Ten), who snapped an eight-game skid against Wisconsin at the Kohl Center. Appling added 16 points.
"They hit some great shots at the end to come back. I don't know what happened at the end, nor do I care," Michigan State head coach Tom Izzo said. "I thought we played well enough and earned the win, and that's the way I'm going to look at it."
Taylor had 28 points for the Badgers (12-4, 1-2), who lost to Iowa on Saturday. Wisconsin has lost back-to-back Big Ten games for the first time since the 2008-09 season.
Trailing by five, 50-45, Taylor pulled up in the lane for a jumper to get Wisconsin within three with 2 1/2 minutes left in regulation.
Jared Berggren blocked Appling's layup at the other end, then made a jumper of his own to make it 50-49.
Berggren came up with another big block to keep the Badgers alive. Taylor made 1-of-2 foul shots with 35.9 ticks remaining to tie the contest.
With the shot clock turned off, the Spartans ran the game clock all the way down. Appling missed a jumper from just inside the three-point line as time expired.
With the score tied at 54-54 in overtime, Michigan State ripped off seven straight points. Derrick Nix made a pair of layups to ignite the burst that Green capped with a pair of foul shots for a 61-54 lead with 31.1 seconds to go.
But Taylor failed to let Wisconsin go down without a fight.
"Without [Jordan Taylor] doing what he did, we wouldn't all be waiting around here so long for a decision," Wisconsin head coach Bo Ryan said.