The Killie striker separated the teams with a 41st-minute header which was sufficient to secure all three points.
It was his eighth goal in five games and it handed Dunfermline their eighth home league defeat in nine games at East End Park.
But, for Kilmarnock, the only way is up as they are now clear of Rangers in fourth place.
Boyd wasted a great chance early on when Andy Tod misplaced a header into his path but he was blinded by his own headlines and lashed a volley well wide.
It was a careless miss and it could have been more costly had Alan Combe not produced a superb fingertip save to keep out an Iain Campbell shot which was bound for the corner of his net.
Boyd netted four minutes before the break when he timed his run to perfection to meet an Allan Johnston cross and steer a header past Allan McGregor.
Tod almost equalised just before the interval when he managed to get his head to a Campbell corner but his effort flashed wide.
Boyd set up Colin Nish early in the second half when he headed a Danny Invincibile cross into his path but McGregor blocked his shot.
Dunfermline threw Tod forward in the second half to give them more of a threat in the air and it almost paid off when he reached another Campbell corner but sent his header wide.