The Citizens skipper had seemingly put the game to bed with a first-half brace, but Rodrigo gave the Whites a slice of hope late on in Sam Allardyce's debut game, making the champions' win far nervier than it should have been.
As expected, a much-changed City side had the lion's share of possession early doors and pinned all 11 Leeds players back into their own half, but Allardyce's team defended with robustness and offered Joel Robles - making his top-flight debut for the Whites in place of the under-performing Illan Meslier - adequate protection.
A skied Julian Alvarez strike in the 16th minute summed up the hosts' frustrating start to the game, but Robles made himself big to deny Erling Braut Haaland one-on-one just a minute later as Pep Guardiola's side belatedly tested the Spaniard.
Leeds' resistance would not last much longer, though, as with 19 minutes gone, Riyad Mahrez comfortably skipped past Junior Firpo on the right and set up the arriving Gundogan to curl a first-time effort into the bottom corner from just inside the box.
There was no let-up from the champions, and Gundogan turned playmaker in the 25th minute to pick out Kevin De Bruyne inside the Leeds box, but the Belgian's cutback for an onrushing Haaland ended with the Norwegian sending a close-range effort just wide when the Etihad crowd expected the net to bulge.
The De Bruyne-Haaland combination did not work in that instance, but a near carbon copy of the Mahrez and Gundogan link-up allowed Man City to deservedly double their lead in the 27th minute.
As was the case with the hosts' opener, Gundogan charged forward to meet Mahrez's pass, but this time, the captain took a touch before picking out the opposite corner with aplomb from the edge of the box.
Allardyce's team unexpectedly came close to cutting the deficit in half just two minutes later as Weston McKennie rose highest to meet a corner from Marc Roca, and his header into the ground was awkward for Ederson, but the Brazilian palmed the ball into the air and away from danger.
There was time for the returning Phil Foden to send a thunderous volley just over the top before the half-time whistle sounded, and the second 45 started in a similar vein, as Guardiola's side continued their relentless attack in search of more goals.
However, Haaland's off-day continued as the Norwegian smacked a free header against the crossbar with the goal at his mercy just three minutes after the restart, but the offside flag spared his blushes on that occasion.
A slight worry arose in the 54th minute, as Nathan Ake went down with an apparent issue before being replaced by Kyle Walker - an untimely concern for Guardiola ahead of the Champions League semi-finals.
Those who placed bets on a Haaland goal may have thrown their phones at the sofa in the 62nd minute, as the striker made a smart turn from Rico Lewis's defence-splitting pass before letting fly, but his effort struck the post and rolled behind.
Allardyce's damage limitation tactics were proving effective, but the recently-introduced Pascal Struijk send Foden tumbling in the penalty area in the 83rd minute, and Andy Madley wasted no time in pointing to the spot.
Instead of giving the ball to the misfiring Haaland, captain Gundogan stepped up in search of his first-ever career hat-trick, but the decision backfired as the German crashed his effort against the post.
A penny for the thoughts of Guardiola, who was seemingly demanding Haaland to take the penalty, as Rodrigo suddenly halved the deficit in the 85th minute to set up a nail-biting finale, getting a lucky break of the ball off Manuel Akanji and curling home into the bottom corner.
However, City survived a brief added time period to extend their lead over Arsenal on the same number of matches, while a valiant Leeds remain 17th on 30 points and only above the drop zone on goal difference.
Guardiola's side now prepare to tackle Real Madrid in the first leg of their Champions League semi-final at the Bernabeu on Tuesday, while the Whites continue their survival task at home to Champions League-chasing Newcastle United next Saturday.