is there a way to get the applied transaction value in a workflow? I don't see that as a field option in Set Field Value.

Uh... given that you can apply more than 1 transaction - I'd expect challenges around this. What exactly are you trying to solve for?

In vendor invoice i have a field for the sales order. I have another field which i need to populate with the inovoice number that is related to that sales order.

My head is getting twisted up on this, too many record hops. I think approach it in two steps. a) On your SO, create a custom field to store the Invoice transaction. b) Create a custom field on the PO which lookup the Invoice for the same SO. I think it would be easier to script this.

I think it would be easier to script this. Indeed. Trying to pretzel a bunch of logic like the one OP has in their use case would give even the savviest SuiteFlow person a four aspirin headache.