We know Magneto is able to affect even adamantium as shown when he extracts all the adamantium from Wolverine's body.
Is he also able to affect or control vibranium? Has that been shown in any Marvel comic or maybe a crossover with Captain America?
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Magneto is able to use his magnetic powers to affect adamantium which is thousands of time more difficult to manipulate once it has been set into a particular form. Vibranium has no such rigidity or claims of durability.
Vibranium may need specialized tools to manipulate, but has never been shown to be particularly difficult to shape or alloy with other materials.
Vibranium has been seen used in a variety of formats in the Marvel Universe. The Black Panther wore body armor comprised of it, had claws made with it and boots which could absorb vibrational energy making them silent and decrease the damage the Panther took from falls and the Constrictor used them in his weaponized cables.
Non-ferrous metals have been affected by his powers in the past, so there is no reason to believe, despite its properties, it would be any more able to resist than any other non-ferrous metal.
In the panel shown below, Magneto is seen using his magnetic powers to repel:
the Iron Man armor (made mostly of steel alloys at the time),
Mjolnir, the hammer of Thor, which is comprised of the extra-dimensional metal, Uru, and
the shield of Captain America, which is made of proto-adamantium (an undisclosed mixture of adamantium and vibranium) and one of the most durable substances on Marvel Earth-616.
He is able to do this effortlessly, so there is no reason to consider he would be less able to affect the pure form of the metal, should he be confronted by it.
Until recently, there wasn't a definitive answer to this question.
Siefer posted a scan from Black Panther Vol 3 #48, where 'Magneto' states that the vibranium micro-weave in Black Panther's costume prevented him from affecting the iron in T'Challa's blood. This implies that Magneto's powers don't work on vibranium.
However, the 'Magneto' T'Challa interacted with there was just a hallucination on his part. T'Challa was suffering from a brain aneurysm at the time, caused by a severe beating he'd taken from Iron Fist in Black Panther Vol 3 #39. As such, I don't think anything said by this 'Magneto' -- particularly in regard to whether his powers do or don't work on vibranium -- should be considered reliable.
Thaddeus Howze pointed out that Magneto has been shown to move Captain America's shield with his powers, specifically in Super-Villain Team-Up Vol 1 #14.
Magneto's clone, Joseph, was also shown to be able to move Cap's shield in Avengers Vol 1 #401.
However, in New Mutants Vol 1 #40, Magneto said Cap's shield was composed of a substance his powers could not affect.
I consider the latter example a goof on the writer's part, for two reasons. Firstly, Magneto was shown to be able to move Cap's shield in at least one prior issue, as evidenced above, so this scene contradicted existing precedent.
Secondly, it didn't make sense, as Cap's shield is composed of a mixture of a unique steel alloy -- which the Official Handbook of the Marvel Universe dubbed proto-adamantium -- and vibranium.
Proto-adamantium isn't quite the same thing as modern adamantium (like the kind used to lace Wolverine's bones), which Magneto definitely can affect.
Proto-adamantium only exists within Captain America's shield, and is a precursor to modern adamantium, which was created as a result of unsuccessful attempts to reproduce proto-adamantium. However, as a metal that is related to modern adamantium, and described as a "steel alloy" by it's creator, Myron MacLean, proto-adamantium logically ought to be magnetic.
So even if Magneto's powers don't work on the vibranium parts of Cap's shield, he should still be able to move it by latching onto the steel parts, the same way he can move a person by latching onto the iron in their blood. By virtue of this though, Magneto's ability to move Cap's shield proves nothing about whether he can directly affect vibranium or not.
In X-Men Vol 5 #1 though, published in 2019, we finally saw Magneto using his powers to directly affect vibranium for the first time.
Wow this is a really tough one. While there are a few instances back years ago where Magneto and Captain America interact, I could not locate ANY instance where Magneto even attempted to take or manipulate the Shield. Most of the interactions are either non-combat or Captain wins by talking Magneto down using his diplomatic skills.
So I cant reference any canon proof as to yes or nay on this but, Given that the prevailing theory as to the reality of Magneto's powers is that he can create and manipulate localized Electromagnetic fields, it would then stand to reason than even a unique material as vibranium could still be manipulated by Magneto's powers. In some cases Magneto clearly moves non-magnetic materials using his powers, so even if the vibranium resisted magnetism he could create localized fields around the shield and move it that way.
Hope this helps.