World number one Alcaraz had just levelled the contest when disaster struck as he limped to his bench holding his right leg at 1-1 in the third set.
While he continued playing, the US Open champion was clearly hampered but Djokovic was merciless, dropping only one of 12 games to book a spot for Sunday's showdown against either last year's runner-up Casper Ruud or German Alexander Zverev.
It was unclear whether Alcaraz, who skipped this year's Australian Open because of a hamstring injury, was suffering from cramps or injured.
Djokovic will play his 34th Grand Slam final, his seventh at Roland Garros, where he lifted the Musketeers' Cup twice, in 2016 and 2021.
He was facing the ultimate test against Alcaraz, who had bulldozed through the draw, only for the machine to break down in abrupt fashion.
"Tough luck for Carlos. Obviously at this level, the last thing you want is cramps and physical problems in the last stages of a Grand Slam," said Djokovic, who was in his 46th semi-final at a major.
"It was probably difficult for him to decide whether he should retire or continue until the last point but he's a fighter, so respect to him for that."
The much-awaited clash had started with Djokovic going for the throat and breaking for 3-1 before saving four break points and taking the opening set after almost an hour.
With Mike Tyson watching from the stands, both players traded punches and Djokovic was on the ropes in the second set, with Alcaraz playing several spectacular shots.
After an exchange of breaks, the Spaniard levelled as Djokovic overcooked a forehand and it appeared that the momentum had shifted.
"It is not easy to maintain that intensity," said Djokovic, who has now won his last 100 Grand Slam matches in which he bagged the opening set.
"Towards the end of the second set he was the better player. I had to be aggressive, to take the ball early otherwise he would be the aggressive one. He is very fast, very dynamic so I had to match that and do even better, which was very exhausting."
It was, however, the youngest player's body that capitulated first in a contest that could have been a classic.
