A method for congestion control includes receiving at a destination computer a packet transmitted on a given flow, in accordance with a predefined transport protocol, through a network by a transmitting network interface controller (NIC) of a source computer, and marked by an element in the network with a forward congestion notification. Upon receiving the marked packet in a receiving NIC of the destination computer, a congestion notification packet (CNP) indicating a flow to be throttled is immediately queued for transmission from the receiving NIC through the network to the source computer. Upon receiving the CNP in the transmitting NIC, transmission of further packets on at least the flow indicated by the CNP from the transmitting NIC to the network is immediately throttled, and an indication of the given flow is passed from the transmitting NIC to a protocol processing software stack running on the source computer.