Yes, IC is used to design digital systems. But IC (you might see it called Virtuoso) typically fits into a larger digital IC design flow. You create digital cells with IC, then have a synthesizer take a VHDL or Verilog design and map the design into your digital cells created in IC.
To create a large custom ditigal ASIC at the transistor level would take too long, years. Even creating the digital cell library in IC takes a long time. The digital cells have to be captured, layed out, charaterized, tested, revised, optimized, etc.