I am trying to measure the power traces consumed by the fpga alone of the DE1-SoC board, while the system is processing the data. Can I do that by sensing any of the external pins? The measurement should not include the power of the other blocks on board.
I don't think you can measure the fpga power alone using Cyclone V.
You can try to check the DE1-SoC board schematic whether they are provided the voltage sensing in board (at power regulator maybe).