The physical universe would not exist if it weren't for its Creator. I think that everything physical is also bound in time; time also comes from a starting point, a 'will' (you could say) that started the chain of cause and effect.
The thing is that He didn't just create things. He also creates, constantly, the stage of time itself and He upholds the existence, and all the physical properties, of created things (both tangible and intangible to us). Judaism believes that He has given us an element of genuine choice, responsibility, and agency that is an inexplicable miracle just like creation itself. Still, not a moment goes by that isn't held by Him in existence. Not a thing exists that exists of its own right.
If He creates everything, even while not being Himself a 'thing' in that universe, then how can there even be a question about how He affects it?
When the Bible speaks of our Creator, of course it uses descriptions that are meaningful to us in creation, but in no way does it assume that Hashem is the same as anything created. He made it. He made the mouth to be able to speak. So when it says that He said 'let there be light', that doesn't mean that He used a mouth or even sounds that are carried in substance and time... all of which He made :) I think it is just pointing to the concept of His intention, His choice, which is the best we can do of understanding His creating of the world.
Doesn't this make Him seem distant? Far from it. He isn't limited to anything small; Judaism believes that He cares for us, knows us, communicates with us, and blesses us in many details of life. Every breath, every bit of food or water, every friendship we have, everything we learn, is in His hands. And how about the things that happen and seem horrible? That's another question, about the kindness of His wisdom. It doesn't mean He isn't near to those who seek Him. Think about it... everything we are is derived from His creating, we are nothing without this, but in existing and in being blessed... we are more intimately near to our Source than we are to anything nearby us in the world. That is a big thing about thankfulness.
PS Or were you really asking, "How can the intangible create the tangible"?