Playing just his third tournament since returning from four and a half months out with a wrist injury, Alcaraz recovered from a shaky start to defeat Czech Lehecka 7-6 (7-4) 6-4.
It is a second title in a row in the Japanese capital for Alcaraz, who showed patchy form at times but finished strongly.
The Spaniard told Sky Sports: "I'm really happy to be able to lift a trophy again. It's been a while and obviously it's extra special after my injury.
"It was a tough week that I didn't find my best tennis, my best level, but I did find the good solutions and I think that's what matters in the end.
"I would say today was the best match of the week, or at least more consistent the level that I played, so I'm just really, really happy."
Lehecka, ranked 19th, was sharper at the start and led 3-1 but Alcaraz hit back to level at 3-3 and showed his full repertoire of crowd-pleasing shots in the tie-break, winning five points in a row from 2-4.
He made his move in the seventh game of the second set with a break to lead 4-3 and looked delighted after clinching victory.
Alcaraz began the season by winning his seventh major title to complete the career grand slam at the Australian Open, and lifted the trophy in his next tournament in Doha before his injury lay-off.
Meanwhile, top-ranked Jannik Sinner has announced he will be out for the rest of the year as he continues to deal with an injured knee.
Sinner has not played since July when he beat Alexander Zverev in the Wimbledon final. He withdrew from the US Open because of a right knee injury.
"Me, together with the doctors, have decided that I need a course of treatment for my knee, which means that the 2026 season is officially over," Sinner said on Tuesday in a video message on Instagram.
"I also need to think about my long-term career so I will do everything possible to get back 100 per cent."
Sinner risks losing the No.1 ranking while he's out.
"On the advice of his medical team, Jannik Sinner will follow a course of treatment for inflammation in his knee," a statement from Sinner's management team said.
"The decision has been made to have the treatment now to give Jannik the necessary time to recover before beginning preparations for 2027."
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