The 3-point shot was a bigger change than anything in football since the addition of the forward pass. 3 pointers drastically changed how offenses were run and instantly made long-range jump shooters more valuable than all but the best post players. Offense in the post used to be the best shot in the game, by far.
Agree with the poster below who cites the shot clock addition to basketball as a more significant change. Yes, the three has changed the way offense is played, but I think you overstate it in your post. I would say that the rule changes favoring perimeter players have done more to shift the game away from the low post than the 3, and that the shift towards jump shooters has happened more in the past 5-7 seasons than in the preceding ones. Another point is that the impact of the three point line has been relatively gradual: in the first year that the NBA added the rule, no player hit more than 80. In the first year of the shot clock, the average game score jumped over 13 points per team. That has to be the most dramatic rule change, and it makes sense: as we're seeing now in the NFL, only leagues in serious trouble contemplate massive rule changes, and no major American sport was more endagered than the NBA in the early 50s.
As a side point, I would add instant replay / Questec / general intrusion of technology into rule enforcement to the list of most significant rule changes. No, it's not bigger than the forward pass, or the shot clock, or even eliminating kick-offs... and, yes, it's more about enforcement of rules than a new rule per se... but it's the rule trend that's most likely to grow and grow and grow over time.