A controller performs network-wide congestion control in a split architecture network. The controller receives flow statistics from switches for each entity that communicates via the network. The controller chooses a most congested link as a bottleneck link based on a packet loss rate that is derived from the flow statistics and estimated for each entity on each link of the network. The controller identifies a target path in the network that passes through the bottleneck link and carries the most traffic, and calculates a throttling probability for each sharing entity that shares the target path based on the capacity of the bottleneck link, capacity of the first link of the target path, bandwidth consumption and packet loss rate of each sharing entity. The controller then transmits the throttling probability of each sharing entity to the ingress switch of the target path to reduce the congestion on the bottleneck link.