Magento – Add Special Price to Product Programmatically

Try this approach. use the config array that the attribute dropdowns use to change the price of the configurable product. Let's assume that $productId is the ID of the configurable product.

$product = Mage::getModel('catalog/product')->load($productId);
$block = Mage::app()->getLayout()->createBlock('catalog/product_view_type_configurable');
$block->setProduct($product);
$config = json_decode($block->getJsonConfig(), true);
$basePrice = $config['basePrice'];
$min = null;
$max = null;
foreach ($config['attributes'] as $aId=>$aValues){
    foreach ($aValues['options'] as $key=>$value){
        if (is_null($min) || $min>$value['price']){
            $min = $value['price'];
        }
        if (is_null($max) || $max<$value['price']){
            $max = $value['price'];
        }
    }
}
//until here we have the min and max price differences. Now just add the base price.
$min += $basePrice;
$max += $basePrice;

Let's say that $storeId is the store for which you want to update the price $specialPrice is your special price, $sku is your product SKU, $fromDate and $toDate are...well, you get the idea.

Now run this code:

$id = Mage::getSingleton('catalog/product')->getIdBySku($sku);
if ($id) {
    Mage::getSingleton('catalog/product_action')->updateAttributes(
        array($id), //array with ids to update
        array( //array with attributes to update
            'special_price' => $specialPrice,
            'special_from_date' => $fromDate,
            'special_to_date' => $toDate,
        ),
        $storeId //store id to update. If you want to update the global value use 0 in here
    );
}