Yes, as of Feb 3, 2016, the shows are part of the same universe.
We have known for a while that this was a possibility, as the shows are produced by the same group of people, and CBS partially owns the CW. Originally the network execs were less enthusiastic to the idea, but when Supergirl's full-season pickup was announced, it was accompanied by rumors that a crossover might happen.
It has now been confirmed:
CBS announced today that Grant Gustin’s Flash will be crossing over into an episode of Supergirl later this year—a development that’s sure to please fans of both series. While details of what the crossover will entail are yet to be revealed, the episode is set to air on Monday, March 28th. src