The Japanese attacker scored a brilliant late strike to seal an impressive victory for the host, which also had goals through Cacau and Martin Harnik.
Stuttgart controlled the opening first half and deservedly took the lead on 37 minutes as Cacau nodded home from close range. Following a corner, Mexican defender Francisco 'Maza' Rodriguez rose to head the ball wide of the target, but the Germany international intercepted and redirected the ball into the net.
Eleven minutes after the interval, the home side scored a critical second goal, leaving its visitors with simply too great a mountain to climb in order to come back into contention. Following a quick free kick, Cristian Molinaro raced up the left flank and crossed to Harnik, who nodded home a free header.
A minute before full time, substitute Shinji Okazaki fired a tremendous 18-yard strike into the left corner of the net, rounding off an impressive result for the host.
Cacau's opener was a long time coming, and Stuttgart would have deserved to enter half-time with a multi-goal lead. Martin Harnik nearly opened the scoring on 12 minutes, but Ralf Fahrmann did just enough to take the pace off the ball, and claim possession just before it crossed the goal line.
On the stroke of halftime, the goal scorer found Harnik wide open at the edge of the penalty area, but Fahrmann was quick off his line and brilliantly blocked the Austrian's shot.
Schalke was not without its share of chances, with Kyriakos Papadopoulos in the 25th minute and Raul in the 28th minute heading narrowly wide in rapid succession. Christian Fuchs earlier tested goalkeeper Sven Ulreich with a blistering free kick, but the Stuttgart goalkeeper did very well to parry.
The visitors were better in the second half, and had they not conceded, might have been able to claim a point. Substitute Julian Draxler had a strong shot from distance saved, and Jan Moravek was twice denied from close range.
The visitors had plenty of possession in the second half, but their high defensive line left acres of open space at the back and Stuttgart had as many close calls as their opponents. Cacau missed a pair of clear opportunities, and Christian Gentner saw his chipped attempt sail narrowly wide. The hosts finally got a deserved third goal, however, through Okazaki's classy strike.
Following its three-goal win, Stuttgart goes level with Wolfsburg on points and goal difference, as leader of the Bundesliga table. Schalke is currently tied with Koln in last place, although they have plenty of time to reverse their woes.
U.S. international midfielder Jermaine Jones started and played 90 minutes for Schalke. Mexican international defender Francisco 'Maza' Rodriguez also played the full 90, for Stuttgart, and redirected a header to Cacau for an assist on his team's opening goal.