Tuesday's victory also earned Alcaraz revenge for a shock loss to Fritz at the Laver Cup in San Francisco this month, the Spaniard's first defeat by the American in four clashes, which came soon after his US Open triumph.
However, Alcaraz's physical issues have prompted him to pull out of the Shanghai Masters, which starts on Wednesday and will feature the return to the ATP Tour of Novak Djokovic
After a high-quality beginning to the match under the roof of the Ariake Colosseum, Alcaraz edged ahead when Fritz sent his shot long to drop serve for the first time, and the top seed was in no mood to relent as he went on to seal the opening set.
Fritz received treatment for a thigh problem before the next set and Alcaraz immediately heaped pressure on the second seed by hitting a blistering forehand to break in the opening game.
The six-time Grand Slam champion quickly built a 4-1 lead, prompting Fritz to throw his racket to the floor in frustration, and although Alcaraz briefly wobbled on serve later, he secured the win for his first Tokyo title.
"I'm really happy with the level that I played and with everything," Alcaraz said.
"Starting the week not really good with the ankle, and the way that I came back from that and played a great tournament, great matches.
"It's been great, my best season so far without a doubt.
"I didn't start the year that good, struggling emotionally, so looking back and how I came back from that."
Early on Alcaraz had responded angrily to being given a time violation.
He said to umpire Fergus Murphy: "Do you think it's normal that I finish a long point at the net and then barely have time to go for the balls, with no time to rest? Do you think it's normal or not? OK, you've never played tennis in your life."
