A joint superimposed sequence design, known as Super-Imposed sequence for PAPR Reduction, or SIPR, using per-tone affine precoding technique is proposed to jointly estimate MIMO-OFDM channels and reduce the peak-to-average power ratio (PAPR) forMIMO-OFDM systems. The proposed technique optimizes the trade-off between BER, MSE of the channel estimate, and PAPR reduction performance. Moreover, it does not require side information to be transmitted for the removal of the sequence at the receiver, and the transmit redundancy can be as small as 1 symbol/subcarrier. The superimposed sequence is designed by solving a convex quadratically constrained quadratic programming problem and has a computational complexity comparable to previous technique using linear programming. It is shown that SIPR can be regarded as a generalization of the popular tone reservation (TR) technique, and thus, is able to outperform TR in terms PAPR reduction performance, with less transmit overhead. Simulation results and transmit redundancy analysis of SIPR and TR are shown to illustrate the efficacy of the proposed scheme.