I don't agree with your choice of runes. Malzahar, with archaic knowledge, doesn't even need that much magic pen, but Having 3 rune types full of just magic pen, doesn't seem like it would end up well for him. Also Abyssal Scepter is a bad choice as well, in my opinion. A void staff would be much more helpful, as it gives more AP and Magic Pen. And as seeing as Malzahar shouldn't be in the middle of a team fight, the Abyssal Scepters effect is not that helpful as you should be staying out of the fight nuking the middle of it. Also I never seem to run out of mana, due to malefics effect of transfering mana after it has killed whatever it was placed on. By mid game, you should be able to clear whole minion waves with that, so the mana regen runes are not that helpful either.

This was all my opinion, but then again I may play Malzahar differently.

Little update with better description for the fight and how to play :)

Barely ever i see him failing with that build, often that nab gets legendary from nowhere...