What were the reasons for Athens' defeat in Peloponnesian War?
Given the scale and time-frame of the conflict, the Peloponnesian War is a deeply complicated subject of study (and, I'd suggest, a discussion on the causes of Athens' defeat would be comparably complex and multifaceted). For one thing, consider that the war itself, dragging on for as long as it did, eventually became a war of desperation for both sides (and, from that perspective, Persian intervention seems to have been critical in securing Athens' defeat). In addition, Athens' war effort was hampered by the factionalism inherent to its own democratic system and by its own strategic mismanagement of the war. In preparing this answer, I have drawn heavily from The Greeks: History, Culture and Society, by Ian Morris and Barry B. Powell (Upper Saddle River: Pearson Prentice Hall, 2006), which devotes its sixteenth chapter to an account of the Peloponnesian War.
When the war began, Pericles was the dominant political voice in Athens and the critical voice in shaping the early phase of the war. Ultimately, Pericles envisioned a Fabian strategy, by which the key to victory was not to engage the Spartan army, but rather to wait Sparta out while maintaining control of the sea to keep its resources and food stores intact. This strategy proved largely successful (Sparta was ultimately unable to overcome Athens' fortifications), but in the process it led to severe overcrowding, resulting in the outbreak of a devastating plague (killing Pericles himself in the process). Pericles' death removed Athens' most influential and important statesman, and his approach was abandoned in favor of more ambitious, high risk strategies. (For more information on this early stage of the war, see pp. 335-337 in Morris and Powell.) This transition is illustrated in one of the war's critical turning points, the Sicilian Expedition, with Athens attacking Syracuse.
The key voice in advancing the Sicilian Expedition was Alcibiades, who was chosen among the expedition's commanders, only to face charges of impiety as the fleet departed. This turn of events proved doubly disastrous: on the one hand, it removed one of Athens' most capable commanders, but moreover, rather than face trial, Alcibiades would defect to Sparta. His influence would see Sparta commit their own forces to Sicily, which would turn into a military disaster for the Athenians, with both their army and fleet destroyed. (For a more expansive account on the Sicilian Expedition and its complicated history, see pp. 344-352 in Morris and Powell.)
Finally, it's important to recognize the role of Persia in determining the winner of the war. As the war dragged on (with both sides exhausted), Sparta agreed to return the Ionian cities to Persian control in exchange for the promise of financial support (though this support would prove limited at first). Later, the ascension of Cyrus to the satrapy of Ionia would secure for Sparta a significant influx of wealth in exchange for promises of military support (when Cyrus would make his own eventual bid to succeed his father as king). This influx of wealth proved critical in shaping Athens' defeat. (This last stage of the war, including Persian intervention, is detailed in pp. 354-359 in Morris and Powell.)