性能 is ability of a mashine in general.
このパソコンは高性能だ。
This PC is Hi-end.
能率 is productivity of human's work.
仕事の能率を上げる道具
Tools that enhance your work performance
There's another word 効率(kouritsu) and it suits to almost every usage of "efficiency".
エネルギー変換効率
efficiency of energy conversion
効率の良いやり方を探す
to look for more efficient method