The season ended when the San Diego Chargers defeated the Boston Patriots in the AFL Championship game – to this date the only major league championship won by the Chargers and the city of San Diego.
The AFL had 8 teams, grouped into two divisions. Each team would play a home-and-away game against the other 7 teams in the league for a total of 14 games, and the best team in the Eastern Division would play against the best in the Western Division in a championship game. If there was tie in the standings, a playoff would be held to determine the division winner. San Diego led the Western Division for the entire season, with Oakland following one game behind from Week Eight onward. The Raiders had started at 2–0, then lost four straight, then began a winning streak. Starting from a 2–4–0 handicap was insurmountable, and although Oakland beat San Diego twice (34–33 on October 27, and 41–27 on December 8), they were unable to catch up.
The Eastern race changed in Week Seven, after the Jets lost to Oakland, 49–26, and the Patriots and Oilers tied at 4–3–0 for the lead. Houston pulled ahead the next week, and Boston beat them 45–3 the week after that; the next week, Boston lost 7–6 to San Diego, while Houston beat the Jets 31–27 to pull ahead again. Two weeks later (Week Twelve), San Diego beat Houston 27–0, while Boston led again after a 17–7 win over Buffalo. In Week Thirteen, Boston was at 7–5–1, and Buffalo and Houston right behind. In the final week, spoiler San Diego took out Houston, 20–14. Buffalo won 19–10 over the Jets, while Boston lost 35–3 to Kansas City, giving the Bills and Pats records of 7–6–1 and forcing a playoff.
The season schedule itself was pushed back a week from what was originally planned, owing to President Kennedy's assassination, which resulted in the AFL moving games from that weekend (i.e., the weekend of November 23–24) to the weekend of December 21–22, 1963. Since only three games had been scheduled for the November 23–24 weekend, with Boston and Buffalo both having a bye, moving the November 23–24 games to December 21–22 meant that the Patriots and Bills finished their regular schedule a week before the league's other six teams did. Consequently, the Patriots and Bills could have played their tiebreaker playoff on December 22, leaving the AFL Championship Game for the next weekend (the originally scheduled date), since they knew after games of December 15 that they and they alone had tied for the division title. But the Bills-Patriots Eastern Division playoff was not played until after the regular season ended, being played on Saturday, December 28 (the day before the Chicago-New York NFL Championship Game). This meant that the Boston-San Diego championship game was not played until January 5, 1964. Thus was held the second professional playoff game ever held in January (with the AFL's first ever title playoff on January 1, 1961, being the only time before then that that had occurred). As it happened, the Patriots-Chargers playoff was also latest date on which a non-Super Bowl playoff game was ever held, and it retained that record until the AFC and NFC Championship Games of January 7, 1979. No 14-game season ever ended later.