The Ghanaian was shown his marching orders in the 61st minute for a second bookable offence on Mako Hasebe.
Schalke 04 ended the game with nine men as goal scorer on the day Julian Draxler also received a straight red card.
Frankfurt also had Slobodan Medojevic sent off making it a total of three red cards shown in the game.
Alexander Meier opened the scoring for away side Frankfurt before Marco Russ doubled the lead to put Schalke 04 2-0 down.
Eric Maxim Choupo-Moting pulled one back from the penalty spot before the first half interval.
Julian Draxler made it 2-2 before he, Boateng and Slobodan Medojivic of Eintracht Frankfurt were sent off in the game.
Schalke 04 have not won a game in the 2014/1015 German Bundesliga season, drawing two and losing two in four game.