Although I doubt that term would be applied to a suicide in a modern country, death records can be unreliable in other times and other cultures when suicide was involved. 100+ years ago suicide was often considered shameful and embarrassing to the family, so it's possible the death record was falsified to protect the family name. Since we have no way of ruling suicide in or out, it's a moot question that I will ignore.
I think the most likely explanation is your relative died of a stroke, head injury or brain tumor that caused increased intracranial pressure. Congestion in the brain usually refers to venous congestion, meaning blood isn't being drained from the brain normally so it's backing up. Venous congestion can be caused by several things but since no mention was made of head injury, the most likely explanation in a 41 year old man would probably be an expanding mass. A tumor that was growing, causing increased intracranial pressure, and possibly physically pressing on the veins that drain the mid-brain region would seem like the most likely explanation.
There are several uses of the phrase "congestion of the midbrain" found in neurology texts and they all occur in the context of expanding masses. I can't copy/paste from Google Books so you'll have to follow the links to read it as text.
Google Books 1
Google Books 2
If you search on the more common English wording "midbrain congestion" you'll find many more references, most of them also discussing brain tumors and other causes of increased pressure within the skull. Google finds no hits at all on the Spanish expression "congestión del mesencéfalo."
Remember, this is completely speculative.