The paper proposes a new approach for FPGA reconfiguration based on usage of the open-source synthesis and place-and-route tools. The well-known partial reconfiguration technologies assume pre-compilation of all required FPGA configurations by the designer. In autonomous intelligent control systems it can become quite a strong limitation, due to control law couldn't be changed on-board without using external FPGA development tool. The paper proposes automatic Verilog code generation and synthesis directly on embedded controller, followed by full FPGA reconfiguration. The experimental results shows, that the resource usage of the FPGA configurations built by open-source tools are comparable to the ones built by well-known commercial toolchain)