Basics
Physiological similarities between organisms describe physical parts that serve similar functions. Fur that keeps mammals warm, for example, is a physiological similarity. Physiology encompasses not just the physical similarity, but the function of said similarity. How an animal eats, how it breathes, how it walks or how it flies are all examples of physiological traits.
Generalizations
Some physiological traits are general to all organisms and are therefore universal similarities. The replication of DNA within cells, for example, is a universal physiological trait of all organisms. Others may not be universal but are still very broad. Sight, for example, is not universal among all organisms (many, like plants, fungi or unicellular organisms do not have sight), but it is very general, as most animals have eyes. Using eyes for sight is a very broad physiological similarity among many organisms.
Physiology vs. Anatomy
Physiology and anatomy both deal with physical structures but differ in that physiology deals strictly with the function of said structures. Both horses and certain lizards have tails, for example, which is an anatomical similarity. However, a lizard may use its tail for balance or self defense, while horses use the tail to keep their hind quarters warm, so they are not physiologically similar.
Behavior vs. Physiology
Behavioral traits should not be confused with physiological traits. Nocturnal behavior is observed in a number of organisms, including bats and owls. However, that is a behavioral similarity, not a physiological similarity. A physiological similarity between bats and owls is that they both use wings for flight.