The Programmer will let you do that. It connects to the ICSP header to access the memory areas directly to make fuse changes.
When you select Sketch:Burn Bootloader, it will change the fuses to the values shown in boards.txt.
For the Uno:
uno.bootloader.tool=avrdude
uno.bootloader.low_fuses=0xFF
uno.bootloader.high_fuses=0xDE
uno.bootloader.extended_fuses=0xFD
uno.bootloader.unlock_bits=0x3F
uno.bootloader.lock_bits=0x0F
uno.bootloader.file=optiboot/optiboot_atmega328.hex