You'll want some sort of waterproof membrane over these holes, so nothing drips inside. I used a disposable rubber glove, as it was both thin and waterproof. Using a very sharp pair of scissors, cut part of the glove in the shape of the two holes and epoxy it from the inside. I would have used hot glue, but I was concerned about melting the rubber. After the epoxy hardens, seal up the edges with some black silicone sealant.
The last picture below is me testing to make sure it was actually sealed.