The unfamiliar line-up briefly trailed after Eldor Shomurodov's opener, but Newcastle United forward Yoshinori Muto's header and Shiotani's thunderbolt gave Japan their third win in the group.
Elsewhere in the group, Oman scored two late goals to down Turkmenistan 3-1 and scramble into the knockouts as one of the best-performing third-placed teams, behind Japan and the Uzbeks.
In the round of 16, Japan will take on either Qatar or three-time winners Saudi Arabia, who face off in Group E, while Uzbekistan take on defending champions Australia.
"The players achieved one of our goals, to reach the knockout stage with three wins and at the top of our group," said Japan coach Hajime Moriyasu.
"It wasn't a risk (to change 10 players)," he added. "I wanted to use these players today.
"We now have some tough games waiting for us so I think it was good that I could use these players and get them match-fit."
Japan had smashed a total of 12 goals past Uzbekistan in their previous two Asian Cup encounters and with only one loss in their last 30 games in the tournament, excluding penalty shoot-outs, confidence was high.
Only Shimizu S-Pulse striker Koya Kitagawa survived from the team that beat Oman but the Blue Samurai still looked sharp with Junya Ito swinging in dangerous crosses from the right.
- Rippling strike -
As Uzbekistan's fans drummed along samba-style, Shomurodov scooped a decent chance over and Japan's Takashi Inui worked veteran goalkeeper Ignatiy Nesterov with a powerful volley.
Nesterov also tipped over Kitagawa's turn and shot before Shomurodov opened the scoring five minutes before the break with a fine piece of work, nudging the ball between two defenders and stabbing home for his fourth goal of the tournament.
But the Uzbek lead lasted only three minutes before defender Sei Muroya's cross from the byline was met by a solid header from Newcastle's Muto, arriving at the back post.
A spell of Japanese pressure early in the second half resulted in a thunderous goal from Shiotani, who plays his club football with Al Ain and unfurled a rippling strike just before the hour-mark.
It knocked the stuffing out of Uzbekistan and when they finally started to press forward again in the final 15 minutes, Japan nearly caught them on the break when Kitagawa blazed over.
With four minutes to go, Davronbek Khashimov caught a shot flush from outside the area and the ball was rocketing towards the top corner before the diving Daniel Schmidt gloved it away.
"It was an incredible save," shrugged Uzbekistan coach Hector Cuper. "But the game was really equal in terms of performance and attitude."
Muhsen Al Ghassani and Mohammed Al-Musallami were on target in the dying minutes in Oman's win over Turkmenistan in Abu Dhabi.
The Gulf side took the lead after 20 minutes thanks to an Ahmed Al Mahaijri free-kick, before Altymyrat Annadurdyyev slammed home the equaliser shortly before half-time.
But Al Ghassani pounced from close range with six minutes left and Al-Musallami added a stoppage-time header to give Oman their first points of the tournament and see them into the knockout stage.