Kirk wore gold. Shatner wore green.
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Here's what you do to answer that question once and for all:
1. Take some film of Shatner under studio lights on the bridge set and develop the film and look at the color of his costume.
2. Take the exact same camera and the exact same lights onto the bridge of the Starship U.S.S. Enterprise and get some film using the exact same film stock of Captain Kirk in his uniform. Then develop that film, bring it back and compare the two pieces of film. (In this little experiment, we control for film stock and lighting and film stock and we make sure we are looking at the two garments in the exact same manner--comparing apples to apples--being careful not to introduce a variability that exists when we look at one garment but not the other. We need to try to control all the variables we can.)
My hunch is that Kirk's uniform in the bridge of the Enterprise would need to be the exact same color as Shatner's costume at Desilu/Paramount in order for our two garments to match when we control for the lighting and the film stock. But that just seems logical to me.