The Java preferences pane moved out of System Preferences with the introduction of Java 7 by Oracle. What was left was a placeholder preferences pane that linked to Oracle's standalone external preferences utility. After a transition lasting years now, it appears that Apple made the decision that the placeholder was no longer necessary.
Still have the Oracle's Java icon in System Preferences. Maybe OP was running original Apple's version of Java and Apple pulled it once and for all during Yosemite install?