i would have to re-read it again but i believe in the book he just disappears. maybe GRRM decided to elaborate a little more on how he did so in the show by showing him jump in the boat.
but in the book...
after Tyrion is condemned to die, however, Varys is forced by Jaime Lannister, at swordpoint, to release Tyrion. He does so, and on the trip through the secret tunnels beneath the Red Keep leads Tyrion past a ladder that the dwarf recognizes as leading to the chamber of the Hand of the King, leading him to inquire how to access his old quarters to seek out his father. Varys makes a curiously weak and obligatory protest against this course of action, advising him to make haste and flee...while also giving precise directions on how to reach Tywin. Tyrion then ascends the ladder to kill his father Tywin. With this outcome and his subsequent arrangement for Tyrion to fit in to his master plan, it is very likely it was more than the threat of violence from a crippled Jaime that caused Varys to release the dwarf. As a loyalist, and knowing Tywin's threat to a Targaryen restoration, plus the fact he attempted to prevent rectification of Cersei's grievous errors, it is most likely he purposefully arranged Tywin's murder, but which strings he pulled and how are currently left unclear as Varys is a master of obfuscation.
Also, When Jaime rescues Tyrion from prison he confesses that Tysha was not a whore but really was in love with Tyrion. This is what makes him decide to go back and see his father for some good crossbow revenge.
