I think in many English sentences they could mean the same thing. IE: They virtually have the same meaning. They essentially have the same meaning. Thesaurus http://thesaurus.com/browse/virtually http://thesaurus.com/browse/essentially

essentially means at bottom or by one's very nature, while substantially means to a great extent or degree or considerably. Example Sentences: It came up with a material that essentially cleans itself, minimizing the need for maintenance. Because they think they can get away with it, and essentially they are getting away with it. These orcas are essentially left with a diseased mouth. Perhaps the first art of virtual communication is choosing which messages to place in which medium. Put bluntly – should I email, should I telephone or should I meet face to face? The more complex the message, the greater interactivity required (either in terms of clarification, discussion or simply engagement) then the decision should be to go less virtual. How can we train this? Well, simply ask your students to print their last ten sent emails and analyse how appropriate it was to send this message via email or whether another channel or combination of channels could have been used. Check out the replies to these emails to see how high the levels of understanding and acceptance are of the original message, and whether time-wasting clarifications and arguments have been generated.