An article from the magazine Kidscreen has verified that Hasbro is ending Transformers Prime with the 13 episode Beast Hunters story line. From AllSpark's Vivid Redshift page scan:

As for Hasbro's established stable of series, which drive the programming on its US joint venture network The Hub, the 13 episodes of Transformers Prime Beast Hunters due to launch this year represent the final chapter of the Transformers Prime story. It has grown to encompass 65 half-hour episodes that continue to roll out around the world. Look for a 75-minute Transformers Prime Beast Hunters movie to hit DVD shelves in Q4.

But that's not the end for Transformers. [Hasbro's SVP of International Distribution and Development Finn] Arnesen says a "new iteration of the animated TV series" is slated for delivery in late 2014, which looks like it might be shaping up to be the year of Autobots, given that audiences are already expecting the fourth live-action blockbuster in July.

Sadly this doesn't come as a surprise as I called this back in October when news first broke of the shortened seasons. Where prime time television considered 100 episodes to be the "magic number" for syndication (Fringe's season 5 renewal is thanks to this line of thinking), for whatever reason cartoon's "magic number" threshold is much lower at 52. The season 3 renewal was probably only because of the Beast Hunters angle to fill the gap to Generations (fall 2013) and Transformers 4 product line (spring 2014). So enjoy it while it last (trailer here) and start speculating on what Hasbro plans after TF4.