There are various ways to do this:

1. If you have the product as ContentData: newProduct.SetValue("MetaFieldName", MetaValue);
2. newProduct["MetaFieldName"] = value;
3. newProduct.Properties["MetaFieldName"] = value; //-for Epi 10+

The recommended way is to have the strongly typed content type for your metaclass, and set it like this:

yourContent.YourProperty = "new value";

ContentRepository.Save(yourContent, SaveAction.Publish);

this works for Commerce 7.5+

Thanks Sapna & Quan for prompt response. Can you please help me a bit more. Let me explain further. Here is my code:

 public class InitializationModule : IInitializableModule
{
      public void Initialize(InitializationEngine context)
      {
           var contentEvents = context.Locate.ContentEvents();
           contentEvents.PublishedContent += EventsPublishedContent; 

      }

}

private void EventsPublishedContent(object sender, EventArgs e)
{

//Here I will call a web service. This web method will return me an id. I need to save this id into current published product metafield.  

}

Please suggest if I can update metafield in above event. Does eventargs holds current published product information? FYI, I have created Metafields, Metaclass through UI only.