Excerpt from: Method, Wisdom and the Three Paths by Geshe Lhundrub Sopa
Question: What is the role of prayer in Buddhism? Does Buddhism believe in prayer, and if so, since Buddhists don't believe in a God, to whom do they pray?
Answer: In Buddhism, prayer means some kind of wishing, an aspiration to have something good occur. In this sense a prayer is a verbal wish. The prayers of Buddhas and bodhisattvas are mental and have great power. These beings have equal love and compassion for all beings. Their prayer is to benefit all sentient beings. So when we pray to them for help or guidance they have the power to influence us.
As well as these considerations, prayer produces a certain kind of Buddha-result. Praying does not mean that personally you don't practice at all, that you just leave everything to Buddha. That is not the case. The Buddhas have to do something and we have to do something. The Buddhas cannot wash away our stains with water, like washing clothing. The root of misery and suffering cannot be extracted like a thorn from the foot. The Buddhas can only show us how to pull out the thorn. The hand that pulls it out must be our own. Buddha cannot transplant his knowledge into our being. He is like a doctor who diagnoses our illnesses and prescribes the cure that we must follow through personal responsibility. If the patient does not take the medicine or follow the advice, the doctor cannot help, no matter how strong his medicines or excellent his skill. A doctor must give medicine to a patient who will take it and follow his advice in order that his efforts will be successful. If we take the medicine of Dharma as prescribed and observe the supportive advices, we can easily cure ourselves of the diseases of ignorance, attachment and the other obstacles to liberation, and also the obstacles to omniscience. To turn to the Dharma but then not to practice it is to be like a patient burdened by a huge bag of medicine while not taking any. Therefore Buddha said, "I have provided the medicine. It is up to you to take it."