The Great Token War is over.

Some time between now and the end of the year, armored trucks filled with some two million Connecticut Turnpike tokens will pull out of Transit Authority headquarters in Brooklyn headed for Connecticut, where the tokens will be redeemed for 17 1/2 cents each.

The agreement, after three years of talks, will mark the end of one of the more acerbic border skirmishes of recent times. The war began in the fall of 1982 when someone discovered that Connecticut Turnpike tokens, worth 17 1/2 cents when bought in rolls of 40, worked very well in subway turnstiles in New York. The subway fare, then 75 cents, is now 90 cents.

Transit Authority officials reacted angrily and began arresting cheaters. Among those caught were briefcase-carrying lawyers and Wall Street three-piece suiters who had been unable to resist making a quick 57 1/2 cents profit a ride.

The battle heated up quickly, with Mayor Koch publicly labeling the cheaters ''lepers'' and ''pariahs.'' Those who came from Fairfield County he called ''rich pariahs.''