Remarkably, this was the fourth time Djokovic had made it this far at the Games and the first time he has come out on top, with a bronze in 2008 his only previous medal.
Now he is guaranteed to better it after defeating Italy's Lorenzo Musetti 6-4 6-2, setting up a rematch of the Wimbledon final, where he was well beaten by Alcaraz .
Djokovic left Roland Garros on Thursday evening very concerned that he had sustained more damage to his right knee, which has been strapped up since he underwent surgery following a meniscus tear at the French Open.
He moved well here but the match was not without drama, Djokovic given two time violations and a warning for an audible obscenity early in the second set.
The Serbian, who had been taken to five sets both times he had previously played Musetti on the Parisian clay, screamed at his box when he twice went a break down but he recovered impressively, finishing with a run of five games in a row.
When Musetti netted a final backhand, Djokovic lay on his back on the clay in delight and relief at having finally cleared the hurdle.
Alcaraz could not have had a more straightforward outing earlier, brushing aside Felix Auger-Aliassime.
The 21-year-old is looking to cap an incredible summer by adding gold to his French Open and Wimbledon titles, and he needed just 75 minutes to ease to a 6-1, 6-1 victory against the Canadian.
"It means a lot to me being in a final at the Olympic Games and giving myself the chance to fight for a gold medal for my country," said Alcaraz. "It is a special moment for me in my career and my life.
"I'm going to try and enjoy this moment but I'm really focused on playing in the final on Sunday. I'm really happy to bring a medal to my country and, hopefully, it's going to be the gold one."
In the women's singles, Iga Swiatek picked herself up following the disappointment of missing out on gold to claim the bronze medal.
The world No1 suffered her first defeat in 26 matches at Roland Garros on Thursday to China's Zheng Qinwen and broke down in tears afterwards during a TV interview.
But she ensured she will go home with something after easing to a 6-2, 6-1 victory over Slovakia's Anna-Karolina Schmiedlova.
Swiatek, whose father was an Olympic rower, said: "I think, had I not played today, I would be crying for a week. I cried for about six hours yesterday, so it was really tough.
"It's sport, it's tennis, usually I am good to understand it's just one part of my life, but this time it was like someone really broke my heart. It's crazy.
"Maybe because I am world number one for such a long time and won so many tournaments, I felt like I can handle everything. But this tournament showed me it is not the case."
There is guaranteed to be a medal for two young Russian athletes in the women's doubles after Mirra Andreeva and Diana Shnaider won their semi-final. They will take on Italian duo Sara Errani and Jasmine Paolini for the gold medal.
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