gistfile1.php

//Display Fields
add_action( 'woocommerce_product_after_variable_attributes', 'variable_fields', 10, 2 );
//JS to add fields for new variations
add_action( 'woocommerce_product_after_variable_attributes_js', 'variable_fields_js' );
//Save variation fields
add_action( 'woocommerce_process_product_meta_variable', 'variable_fields_process', 10, 1 );

function variable_fields( $loop, $variation_data ) {
?>	
	<tr>
		<td>
			<div>
					<label><?php _e( 'My Custom Field', 'woocommerce' ); ?></label>
					<input type="text" size="5" name="my_custom_field[<?php echo $loop; ?>]" value="<?php echo $variation_data['_my_custom_field'][0]; ?>"/>
			</div>
		</td>
	</tr>
<?php
}

function variable_fields_js() {
?>
<tr>\
		<td>\
			<div>\
					<label><?php _e( 'My Custom Field', 'woocommerce' ); ?></label>\
					<input type="text" size="5" name="my_custom_field[' + loop + ']" />\
			</div>\
		</td>\
	</tr>\
<?php
}

function variable_fields_process( $post_id ) {
	if (isset( $_POST['variable_sku'] ) ) :
		$variable_sku = $_POST['variable_sku'];
		$variable_post_id = $_POST['variable_post_id'];
		$variable_custom_field = $_POST['my_custom_field'];
		for ( $i = 0; $i < sizeof( $variable_sku ); $i++ ) :
			$variation_id = (int) $variable_post_id[$i];
			if ( isset( $variable_custom_field[$i] ) ) {
				update_post_meta( $variation_id, '_my_custom_field', stripslashes( $variable_custom_field[$i] ) );
			}
		endfor;
	endif;
}