Jota's late winner earned Celtic a first away Scottish Premiership victory since February as Aberdeen's winless run extended to nine games.
Kyogo Furuhashi chested in a deserved early opener but the hosts improved after the break and equalised when Lewis Ferguson diverted a corner in.
However, the visitors responded late at Pittodrie as Jota's close-range finish earned a long-awaited away win.
The result means Celtic remain sixth and Aberdeen stay ninth.
But Ange Postecoglou's side have closed the gap on the pack above, but still sit six points adrift of league leaders Rangers.
Aberdeen are without a win in all competitions in nine games, which includes a four-game losing streak in the Premiership - their worst run in the top-flight since April 2011.
All the pre-match talk about a Scott Brown reunion clouded the fact both sides were in need of a morale-boosting win, and for the majority of the first period, it looked like the visitors were the only team looking to achieve it as Aberdeen struggled to deal with Celtic's tempo and approach play.
David Turnbull curled in a corner to Nir Bitton who squandered a golden close-range header but Kyogo made up for the Israel player's miss when the Scotland midfielder bent in another stunning cross to find the Japan forward, who casually chested the ball into the Aberdeen net.
Celtic were clicking, especially down the right as young Aberdeen full-back Jack MacKenzie struggled to deal with Turnbull and Liel Abada doubling up on his side.
But it was the opposite flank that almost brought a second goal, Jota chopping inside and unleashing a dipping shot that bounced off Gary Woods' bar.
The home side took a while to get going, but came to life as the first half came to a close.
Celtic's defence showed signs of creaking as Christian Ramirez found himself with acres of space at a corner and hit a volley into the ground which Joe Hart flapped at before seeing the ball clip the bar.
Aberdeen continued that improvement into the second half with more direct play as Austin Samuels flashed over.
The hosts got the equaliser their second-half showing merited when Calvin Ramsay's corner found Ferguson, who rose highest and ended up diverting the ball in with his shoulder.
The hosts might have taken the lead, with Hart parrying away a close-range header from Brown and a strike from Jonny Hayes.
But Celtic were more composed in the latter stages and found a vital winner when neat build-up on the edge of the area resulted in Adam Montgomery sliding the ball across for Jota to make no mistake.
Man of the match - David Turnbull
What did we learn?
Questions have rightly been asked about Celtic's mentality when the chips are down, and when Aberdeen equalised Postecoglou might well have been fearing the worst.
But his side showed a mental toughness that has until now been rarely witnessed and the Australian will hope this is a turning point in his side's campaign.
For long periods of the first half it looked like Aberdeen would fail to capitalise on Celtic's vulnerable backline, but Glass' men rallied in a much-improved second half.
In isolation, a home defeat to Celtic is not catastrophic, but with the run the Dons are currently enduring and the mindset Glass' players must surely be currently experiencing, this felt like a dispiriting moment in the Pittodrie side's campaign.
What did they say?
Aberdeen manager Stephen Glass: "Overall we're disappointed, but I'm pleased with the second half.
"We're concerned we're not getting the points we deserve on the board. It's important we keep trying to get it right."
Celtic boss Ange Postecoglou: "The second half was a real battle, to the players' credit we were looking for that second goal and I'm pleased the players got their reward.
"The important thing is the manner we did it, we showed great character. That's probably the one thing people were questioning up until now."
What's next?
Celtic go to Motherwell on 16 October (15:00 BST) after the international break, as Aberdeen travel to Dundee (18:00) on the same day.