do u know taht super man if he flies at the speed of 1% of lightspeed, he will be travelling at 7 million miles n hour. as the fight starts, he circles the globe (at the equator the earth is about 21,600 miles) so he takes off. in 11 seconds (if they are fighting on the equator) mags starts drawing electromagnetic force to him in massive shield and prepares for the attack. of course, supes speed has also thrown off the EM forces on earth (mach 10 causes severe disturbances (mach 9090 will be catastrophic))
mags gathers his strength and they collide head on. now, the impact of supes PUNCHING mags at mach 9090 and mags hitting supes with the power he could muster will be nothing short of an extinction level event impact. mags will be disintegrated and the impact will knock supes into orbit where eh will remain unconscious for an hour or so.
everywhere in supes flight wake will be destroyed for 100 miles around and the impact zone will be akin to a multi megaton warhead explosion at ground zero.
supes wins
regardless, even if supes didnt do that, he reaction time is so much faster than magnetos that he can stomp him b4 mags realized he moved