This is all the counterplay I could find for Malzahar:
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You can pop his Banshee's Veil with an auto attack before you use your spells.
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You can kill his minions in one hit for easy gold. This will also cripple his wave clear.
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If you stay away from minions who are about to die with his Malefic Visions on them, you won't get hit by it.
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You already pointed this about but I am afraid the only counterplay (that you can do) to his ult is either buy QSS or play Gangplank.
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Malzahar can't perform any other actions while he is ulting you, allowing your teammates to focus him down.
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He has no tank stats and mobility at all and if locked down he is an easy kill.
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Buying magic resistance items also help reduce his damage output and Adaptive Helm is especially great since it gives 20% damage reduction to his E and Ult in addition to the damage reduction already given by the magic resistance from QSS aswell as Adaptive Helm.
Overall I'd say there is a lot of counterplay to Malzahar.
Edit: Added a 7 counterplay option and removed the part where it said his minions were part of his kill potential.