The Brazilian came on at half time, converted a penalty six minutes later and was given two yellow cards — the first for tussling with Bayern goalkeeper Sven Ulreich in the net — within four minutes of each other.
Bayern moved closer to a seventh consecutive Bundesliga title as it put them on 74 points, five clear of Borussia Dortmund who visit Werder Bremen later on Saturday. Both teams have two games left after that.
Hanover were spared relegation for at least another week because VfB Stuttgart, who are in the relegation playoff spot, lost 3-1 at Hertha Berlin, leaving them six points clear of Thomas Doll’s team.
Robert Lewandowski headed in from Joshua Kimmich‘s cross in the 27th minute and Bayern were cruising when Leon Goretzka scored with a low shot from the edge of the area, perfectly placed just inside Michael Esser‘s near post, in the 40th minute.
Kingsley Coman curled a ball just wide and Goretzka contrived to fire against the crossbar from six metres as Bayern threatened a rout.
Jonathas converted but then pushed Ulreich as both players tried to collect the ball from the net.
Shortly afterwards, Jonathas was sent off for hitting Kimmich in the face as they went for the ball, although it appeared unintentional.
Bayern struggled against 10 men but finally sealed the points with six minutes left through veteran substitute Franck Ribery who collected a Coman pass, cut inside and scored with a deflected shot