City have cruised to the top of the Premier League - netting 29 goals in eight league games this term - and any claims that Serie A's own in-form leaders could halt the hosts' fine run looked to have been put to bed inside the opening quarter of an hour at the Etihad Stadium.
Guardiola had predicted a "fascinating" contest and that it was, but poor Napoli initially had no answer to City's rampant attacking play as Raheem Sterling and Gabriel Jesus scored early on.
Maurizio Sarri ignored his president's calls to rest key men for this match - with second-placed Inter visiting the San Paolo this weekend - but Dries Mertens' first notable contribution was to see a penalty saved.
However, as City stepped off the gas after the break, Napoli hit their stride and a second spot-kick - from Amadou Diawara - was converted to set up a dramatic finish.
The visitors could not then force an equaliser, but their second-half dominance will have given Guardiola food for thought as his side move on to nine points; the Etihad crowd certainly felt their nerves jangling in the closing stages.
City have never played out a goalless draw in a group game in this competition and it quickly became clear that Guardiola's unchanged side would maintain that entertaining record in a stunning display.
Sterling swept a finish beyond the wrongfooted Pepe Reina - for his eighth of the season - after Kyle Walker's close-range shot was blocked, with a second goal following just four minutes later through Jesus, who converted from Kevin De Bruyne's low, sweeping centre.
Having won each of their previous three home league games by a margin of five, City's momentum did not slow.
Sterling delayed his pass as the relentless hosts broke in numbers after a rare Napoli foray, but Leroy Sane had the patience and awareness to then pick out De Bruyne on the edge of the area for a thunderous drive that rattled the underside of the crossbar.
Goal-line technology confirmed that the Belgian's effort had not crossed the line and referee Antonio Mateu Lahoz was again checking his watch when Reina and Kalidou Koulibaly combined to scramble Jesus' strike away from the goalmouth.
Napoli looked to have been handed a route back into the game towards the end of the first half but, when Walker dragged Raul Albiol down, Ederson blocked Mertens' penalty and Fernandinho hacked clear.
The visitors momentarily gained a foothold in the tie, despite the miss, but only a vital Reina block kept Jesus from further extending City's lead.
10+ - Napoli have faced 10+ shots in a Champions League first half only five time, three of them against Manchester City. Shock. — OptaPaolo (@OptaPaolo) October 17, 2017
Although Napoli kicked on after the restart, forcing the home side back, chances for Sarri's men were initially few and far between and they were dealt a blow just before the hour mark as Lorenzo Insigne hobbled off.
City were seemingly caught out by their opponents' vast improvement, though, and Marek Hamsik looked destined to equal Diego Maradona's all-time Napoli scoring record when Mertens squared to his captain - with Ederson grounded - only for John Stones to make a brilliant diving block.
But the visitors did not have to wait much longer for their goal. Fernandinho's foul on Faouzi Ghoulam resulted in a second spot-kick and Diawara took on the responsibility, finally ending a run of six consecutive Champions League penalty saves from City goalkeepers.
Jesus thought he had restored the two-goal lead but strayed offside from De Bruyne's pass, before the midfielder tested Reina with a free-kick and Mertens dragged wide at the other end.
City saw out the victory, but they know they must head to the San Paolo in a fortnight - that prospect will feel rather more daunting now than it did at half-time, even if they need only a point in Italy to secure their progression.
Key Opta stats:
- In all competitions, Manchester City have now recorded 10 consecutive victories; equalling their previous best run under Pep Guardiola (10 wins at the start of 2016-17).
- Manchester City have won their opening three games of a European tournament for the first time since 2008-09 (in the UEFA Cup), however this is the first time they have achieved it in the Champions League.
- The Citizens have also won three consecutive home games in the Champions League for the first time, and are now unbeaten in their last 11 overall (W8 D3).
- Gabriel Jesus has been directly involved in 21 goals in 20 starts in all competitions for Manchester City (15 goals, 6 assists).
- Raheem Sterling has already scored 8 goals in 11 appearances for Manchester City this season; two fewer than he did in 47 appearances last term (10).
- Manchester City goalkeepers have saved six of the last seven penalties that they have faced in the Champions League (three by Joe Hart, two by Willy Caballero and one by Ederson).
- Manchester City's starting XI tonight was their youngest in the Champions League under Pep Guardiola (26y 73d), and their youngest in the competition overall since October 2012 (25y 309d v Borussia Dortmund).