That was never made clear in the current timeline. The only hint of how Skynet was defeated appears in the very first film, when Kyle Reese is being interrogated by Silberman. When asked why Skynet had sent back the Terminator, Kyle replied: "It had no choice. Their defense grid was smashed. We'd won." I would assume the next two films will address how Skynet was defeated. In T2-3D, however, the Terminator and John Connor entered Skynet's system core and the Terminator destroyed it as John went back to the present.