Beikhokhei struck the winner in the 63rd minute by skillfully foxing two rival defenders and then played well with Lalhlimthra to finish off with a firm right footer that ended the campaign of five-time winners Kerala.
Kerala looked lacklustre as Mizoram dominated the show at the Salt Lake Stadium for the major part of the game.
The Mizos could have gone ahead in the later stages of the opening session, but David Lalrinmuana's power-packed left footer found the crosspiece in the way.
Mizoram will play Tamil Nadu in their maiden quarterfinal game.
On Thursday, title holders Goa will lock horns with Karnataka, while Services will take on Punjab in quarterfinal exchanges.