Lance Stroll made another strong launch to gain two places on Lando Norris and Yuki Tsunoda, with George Russell promoting his Mercedes into the points with a similar gain.
Further back Valtteri Bottas was squeezed further back and dropped five places down to 18th as Alex Albon made slight contact with Oscar Piastri’s McLaren.
Nevertheless, all the cars still managed to make it through the opening exchanges still in the running and without a trip needed to the pits for any repairs.
Having survived the first lap without sustaining damage to his RB19 unlike in yesterday’s race, Verstappen instantly stuck to the rear of Leclerc, denying the Ferrari driver the opportunity to scamper away in the nascent stages as he had in the Sprint.
Despite a shortened DRS zone for this year’s race, Leclerc was powerless to defend from Verstappen’s Red Bull once the slot in the rear wing opened and the reigning champion blasted into the lead.
Unsurprisingly, Perez would swiftly repeat the move on the Ferrari down the start-finish straight that won him Saturday’s 17-lap dash to settle into second, and still within touching distance of his team-mate out front.
Pierre Gasly and Bottas were the first drivers to pit as both Alpine and Alfa Romeo opted to dispense with the medium tyre early in favour of the more durable hard compound.
That move prompted a flurry of activity down in the pit lane, with the hardest rubber available for this weekend being the preferred choice among all of the teams.
Fernando Alonso spotted as early as the sixth lap that Hamilton – stuck in the turbulent air of Carlos Sainz – was already developing graining on his tyres, and the Brit was the first of the front-running cars to tail into the pit lane to fit a fresh set.
However, the seven-time champion came out in 12th place and within a train of several cars still yet to stop in the midfield.
A string of strong lap times as the counter ticked into double digits hauled Perez within one second of Verstappen, granting him the platform to activate the DRS mechanism.
But the two-time title winner dived in and out of the pits right as a Safety Car was called for the stranded AlphaTauri of Nyck de Vries, whose miserable start to his rookie campaign continued.
Replays showed de Vries clipped the inside wall at Turn 6, breaking his suspension and sending him into retirement for the second race running.
The neutralisation of the race enabled all those who hadn’t already pitted to effectively make a free stop for new tyres, promoting Perez into the lead as Leclerc also nudged ahead of Verstappen.
Russell was also a huge benefactor of the timing of the Safety Car to rise to sixth, but team-mate Hamilton was caught out with his earlier stop and dropped down to P10.
Upon the race returning to green flag conditions at the start of Lap 14, Perez’s defence of Leclerc into Turn 1 put the Monegasque racer out of position and opened the door for Verstappen to regain second position on the inside into Turn 4.
Both Aston Martin drivers, meanwhile, were on the move as Stroll jumped back ahead of Russell while Alonso made an opportunistic manoeuvre on Sainz into Turn 6.
Russell’s sluggish restart resumed as Hamilton dove past the sister Mercedes into the first turn before the elder Brit mounted a successful attack on Stroll, pouncing on the Canadian suffering a slight understeer moment at Turn 16.
Ocon and Hulkenberg, who had been withdrawn to the pit lane for the start to make set-up alterations, were still running on the hard tyre they selected for the start at this point and completed the top 10 as proceedings reached the halfway stage.
With the Red Bull package once again being the class of the field, it quickly developed into a duel between Perez and Verstappen for the honour of standing on the top step.
Despite setting the fastest lap soon after the Safety Car period, Verstappen was unable to get within DRS range of his team-mate and direct rival for the victory.
While the gap floated above one second for several laps, Perez soon gradually began to pull away to increase his leading margin to over two seconds with 20 laps to run.
As the fight for the win deteriorated, Alonso, aiming for a fourth consecutive F1 podium, briefly closed on Leclerc and looked set to ignite some action in the closing laps.
However, the Aston Martin car dropped back suddenly thereafter, confirming that Leclerc would arrest his slump in form with a maiden trip to the rostrum in Baku.
Sainz in the second Ferrari had admitted after the Sprint it was a “damage limitation” weekend for him after troubles with the rear of his SF-23 and that was evident again on Sunday as the Spaniard was unable to live with the pace of his team-mate.
But Sainz was able to resist the threat of Hamilton looming large in his mirrors for the majority of the second stint to finish fourth, with Stroll classified sixth ahead of Russell.
Norris had been left frustrated behind the long-running Hulkenberg but the McLaren ace was finally able to overtake the Haas at Turn 7 before his mandatory pit stop.
Ocon’s solitary trip to the pits in the final laps promoted Norris a further place to ninth in the heavily-improved McLaren MCL60, with Tsunoda also notching a point for AlphaTauri for the second consecutive race.
Despite failing to repeat its podium-scoring heroics from Australia, Mercedes collected the additional bonus point for the fastest lap by stopping Russell for a second time.
Following his victory in the first Sprint event of the year yesterday, Perez’s second win in Baku has reduced his deficit to Verstappen in the Drivers’ standings to only six points.
Next up on the calendar is the second running of the Miami Grand Prix – a race in which Verstappen won in its inaugural running last year.