The decision comes after the show's second run struggled in the ratings, according to Deadline.
Recent episodes of the spinoff have attracted around 1m viewers, down on the 2.3m that watched the pilot episode in 2009.
Syfy's decision will mark the end for the Stargate television franchise, which began with Stargate SG-1 in 1997.
The remaining ten episodes of SGU's second season will air in the spring.
Executive producer Joseph Mallozzi previously revealed that the show's production team had planned out a five-year story arc.