Kevin Magnussen dropped a couple of places to Pierre Gasly and George Russell, while further back there was contact as Nyck de Vries locked up and went into Lando Norris at the first turn.
However, Oscar Piastri in the sister McLaren was the biggest gainer of all, making optimal use of the soft tyre to move up five spots.
The opening foray to Logan Sargeant’s home F1 debut hadn’t gone to plan as the American was in the pits for a new front wing, with McLaren abandoning its soft tyre gamble on both cars only a few laps later.
Verstappen, starting on the hard compound, made a tentative start and failed to gain a spot on the opening lap, with Lewis Hamilton also only able to hold position in P13.
But the reigning champion was soon on the march and picked off the Alfa Romeo of Valtteri Bottas before mounting a double move on Magnussen and Charles Leclerc into Turn 1 to rise to sixth by the beginning of Lap 4, as the Ferrari-powered duo continued to dice with the Dane coming out on top.
Next up on Verstappen’s radar was George Russell and he duly made a comfortable pass stick on the Mercedes driver using the aid of DRS on the back straight four laps later, then overtaking Gasly’s Alpine for fourth the next time around with a carbon copy move into Turn 17.
Russell took advantage of Gasly being compromised to slide on through up the inside of the first corner with a late lunge that promoted him to fifth.
The Brit’s Mercedes team-mate wasn’t faring quite as well with getting his way through the midfield traffic, with the drivers’ worst fears realised as DRS trains quickly formed behind Bottas, aiming for points for the first time since the first round, in the lead Alfa Romeo.
Leclerc had been held up by Magnussen for several laps since their early close-quarters battle and the Ferrari ace was frustrated once more when an overtaking move into Turn 1 was rebuffed.
Shortly after, Leclerc was finally freed when the Haas pulled into the pits at the end of the following lap, triggering a series of stops that included Gasly and Bottas coming in.
Meanwhile, Perez began to increasingly extend his margin to over 3s to Alonso behind, as Verstappen moved into the podium places by Lap 15 with an easy move on the defenceless Carlos Sainz.
Alonso had predicted Verstappen would be in his mirrors by Lap 25, but the Spaniard’s estimations proved to not be accurate this time around as the Red Bull flew past the Aston Martin 10 laps earlier than he had anticipated after qualifying.
The Aston Martin was uncharacteristically struggling on its tyres compared to the Ferrari and the Italian outfit was able to execute a successful undercut to propel Sainz ahead of Alonso into a net third.
With the hard tyre being reported as the favoured race tyre, Verstappen rapidly reduced Perez’s advantage down to just over 1s by the time Red Bull fitted the Mexican with fresh rubber.
Having qualified a lowly 18th, Lance Stroll was running to aim long on the hard tyre, but his strategy was already appearing to be a forlorn one as he dropped out of the points places with Russell and Gasly making light work of the Canadian.
On the other side of the garage, Aston Martin, recognising that Sainz was going to poach the place with an earlier stop, ran Alonso’s first stint six laps longer than the Ferrari and he reaped the rewards to swoop back past his compatriot.
Sainz’s race unravelled further when his push for the podium was knocked by the confirmation he had picked up a five-second time penalty for speeding in the pit lane.
Russell continued on the attack in his Mercedes and made his way through Yuki Tsunoda, Nico Hulkenberg, team-mate Hamilton – via a team order – and Esteban Ocon to leave him hunting down Sainz.
Ferrari’s troubles continued as Russell made the move on Sainz, while Magnussen continued his fight with Leclerc by launching a counter-pass into Turn 1 after being overtaken three corners earlier.
However, Leclerc learnt his lesson by biding his time and completing a move into the first corner on the next lap to finally break the Haas man’s staunch resistance.
Back at the front, Verstappen continued to pump in competitive lap times and his pursuit of the win was aided by Perez losing one second in a single lap, leaving the two-time title winner only 1.2s behind his team-mate once he pitted at the end of Lap 45.
Equipped with new medium tyres, Verstappen soon reeled in Perez and completed his remarkable comeback with a pass around the outside of Turn 1 at the start of Lap 48 to become the first F1 driver to win from ninth on the grid since Niki Lauda at the 1984 French Grand Prix.
The additional bonus point for the fastest lap means Verstappen now possesses a 14-point lead over Perez, with Alonso’s third-place finish consolidating his position behind the Red Bull duo in the standings.
Hamilton in the other Mercedes came on strong in the second stint to make a multitude of moves to be classified sixth, including on Leclerc in the closing stages.
Alpine moved on from successive nightmare weekends in Australia and Azerbaijan to bring two cars home inside the points as Ocon wound up ninth, with Magnussen holding on to claim the final point for Haas.
F1 now embarks on a two-week break ahead of its return to Europe with the Emilia Romagna Grand Prix at Imola.