Hello Saurabh,
you can try to enable gigabit flow control on both sides so that your switch port can send IEEE pause frames to signal to the server port to be silent for some time to give time to empty the port buffers.
Or better by rereading your post it is the server that can send pause frames to your switch port.
By the way what platform and linecard is involved ?
Be aware that some linecards like WS-4548 for 4500 have one ASIC to serve a group of 8 ports that is 8 ports share 1Gbps bandwidth inbound and outbound.
Similarly some linecards of C6500 have a similar architecture.
We have found this during a performance test.
Flow control can help
Hope to help
Giuseppe