How to set price field value programmatically in Drupal Commerce

Price in Drupal Commerce 2.x is not a number but a class. This class has a price number and currency code properties, and both are strings. So, to set the product price programmatically you have to first instantiate the Price class:

$price = new \Drupal\commerce_price\Price('9.99', 'EUR');

and then use created Price object to set the product price:

$product_variation = \Drupal\commerce_product\Entity\ProductVariation::load(1);
$product_variation->set('price', $price);
$product_variation->save();

To get the price number and currency code you can use appropriate getters methods:

$price_number = $price->getNumber();
$currency_code = $price->getCurrencyCode();

You can also create a Price object by using the static method:

$price = Price::fromArray(['number' => '9.99', 'currency_code' => 'EUR']);