I would interpret them the same way. However, you would almost always see the first one used. This is because it is much easier to misinterpret the second. If you say it with a pause in the wrong place, it becomes: the election was so bitterly contested that a special electoral commission was given the authority to determine the candidate, who had won. In such a case, the commission would not determine which candidate won, but would just determine the candidate - who also won, by the way. It's a small difference, but just means the the first sentence has no chance of being misinterpreted.

They have the same meaning, but the first answer is better and more precise ("...which candidate had won.").

fdmaxey gave an excellent answer, especially by mentioning how the second example could be more easily misunderstood. i would just like to add; by using "who" as per the second example, you are being more personable in the way that you refer to winning candidate. by using "who", you talking about them as a person rather than just "a candidate" (thing / object / job function).