The microcontroller performs the task of minimization of peripherals on the PCB by miniaturization and integrating them in one housing.
FPGA on the other hand is used to implement digital logic. Since FPGA can be programmed in a remote location using standard tools. And the growing market of the FPGA has made the tools required to program and debug very affordable.
There are microcontrollers that have FPGA built inside of them. They can implement very small digital logic. But that will result in the minimization of components on the PCB.
They bridge the gap between a dedicated FPGA and a microcontroller. For small applications which only needs a very small custom logic design, they can be used.
Programmable System-On-Chip (PSoC) from Cypress semiconductor and C2000 TMS320F28379D from Texas Instrument are such examples.
The FPGA can be used to implement the Finite State machines Logic.
The microcontroller manufacturer also provides additional peripheral which can be connected in a customized fashion using the crossbar interconnects to make a custom peripheral. And since the logic is not outside there is high security.
FPGA provided on these microcontrollers cannot replace the traditional FPGA.
PSoC from Cypress is highly configurable and along with digital logic, it also has analogue peripheral such as op-amps and comparator which can be used to create custom logic.
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