A defining feature of sleep is its homeostatic control, which is most clearly expressed as increased sleep after forced wakefulness. Drosophila has served as a powerful model system for understanding the homeostatic control of sleep and ongoing work continues to be an important complement to studies in mammals and other vertebrate models. Nevertheless, there are significant challenges confronting investigators of sleep regulation in Drosophila. For example, the magnitude of sleep rebound in flies is relatively modest, providing a small dynamic range over which to detect changes in homeostatic responses in experimental subjects. In addition, the perturbation necessary to keep flies awake is associated with physiological and behavioral responses that may obscure homeostatic sleep responses. Furthermore, the analysis of fly sleep as a unitary state, without differentiation between shallow and deep sleep states, clouds our ability to fully characterize homeostatic sleep responses. To address these challenges, we describe the development of a yoked-controlled paradigm for flies that allows us to produce two sets of flies that have experienced identical levels of mechanical perturbation while suffering significantly different amounts of sleep deprivation. Moreover, by differentiating long bouts of sleep from all sleep, we show that flies display significant and lasting homeostatic increases in such long bouts following sleep deprivation, that are only detectable when controlling for the sleep-independent effects of mechanical deprivation. Finally, we illustrate the importance of yoked controls for examining the molecular correlates of sleep pressure. Our work introduces methodological approaches that are likely to support the discovery of new mechanisms of sleep regulation in the fly and calls for the reevaluation of previous work identifying the molecular, physiological, and cellular correlates of sleep pressure.