Pick Nasus with Phase rush and W malpite everytime he q you, go in make a short trade-proc phase rush- and walk out to last hit minions and lifesteal your hp back to full.
Pick Jax with conq cause everytime malphite will come close to you after he Q you to proc his W you open your stun and beat him up. Malphite must choose either back off in order to avoid taking free damage or stay near and get beaten.
Pick Garen cause his Q apply a slow cleanse and a speed boost. So he Q you -ok Q and walk back and wait for your passive to heal you up.
Pick Camile and stand close to walls that way you have access to E away or chase back Malphite and if you time your ultimate you can dodge his ultimate which it still is the Malphites bread and butter. Camille passive will helps her for short treades and she has 2 auto attack resets in her Q plus true damage. So in any case you outduel him in short trades in early and can deal him after 6.
Pick gnar with glacial augment or Phase rush. Everytime he q you and want to come close to damage you then use Q auto then jump backwards and if Maplhite still chases auto 3ed time and get the movespeed from gnar s W. If you are in mega gnar just cc him to death
Pick Renecton with conq. Stun him with his W and Q you heal from Malphite and dash backwards to disengage or forward to commit. With conq up you outdamage him and outheal Malph damage.
Pick RIven with conq. She has 4 dashes and 1 stun, 1 knock up and shield. She can choose if she wants to fight malphite or not. Malphite can just wast mana on you to try to damage her but Riven can just shield the damage. Unless you mess up as riven you should be able to win lane. I mean riven even with the nerfs in her shield CD she still a very stong pick.
Pick Kennen with Phase rush. You outrange him so hard and you can proc your Phase rush on malph so easily that its laughable. AND kennen has his E which is his i-dont-want-to-fight button so he can go back and come back in whenever it pleases.
Pick jayce. You dont want malphite be close to you then go melee form and E him away ( its a knock back) and then go range use E and leave like a boss. You want to chase malphite you start with range E Q combo and then go melee and Q him ( its jumps towards the target).
PS I assume that the top lane is strictly 1vs1 with no jungle help or roaming from other lanes. Now they are ap picks like lissandra, Ryze and Vlad that can handle malphite and kite him and scale into late game.