Red Bull had pulled off a masterstroke in pitting under the safety auto, giving their drivers the advantage of fresh tyres in a newly bunched-up field.
The four-time world champion has always professed his love for F1's most famous team - Ferrari - and if they are on course to return to the top of the sport and with Vettel's teammate Kimi Raikkonen out of contract at the end of the season, there could be possibility of the British driver making the switch over to the Maranello based team.
Verstappen's day was not done there, however.
On lap 43 he saw an opportunity to overtake at the Turn 14 hairpin.
The Red Bull driver took fifth after being handed a 10-second penalty and, while measured in his response, Vettel was keen to remind Verstappen, 20, that he was no longer a rookie. Mercedes teammate Valtteri Bottas was third in both sessions.
His teammate Verstappen had a more dramatic time of things.
That allowed him to cut Sebastian Vettel's overall lead from 17 points to nine, with the Ferrari driver finishing only eighth. Kevin Magnussen, who starts P11, will nearly certainly start on the soft tyre and should make some progress by running a longer first stint.
It was also only Ferrari's second in Shanghai after Rubens Barrichello started the inaugural Chinese race from the front in 2004.
Despite going for his fifth Chinese GP pole position, the British racer qualified a disappointing fourth in Shanghai on Saturday.
Valtteri Bottas was over half a second slower than Vettel.
"The balance of the vehicle is good but we have some fine-tuning to do on it tonight".
But the race took a second dramatic twist when the safety vehicle was deployed following a coming-together between the Toro Rosso pair of Brendon Hartley and Pierre Gasly on lap 31.
But Daniel Ricciardo was the focus of Q1 as the Australian required a total engine rebuild after FP3.
Ricciardo's progress from that point was masterful.
The contrast between Ricciardo and Verstappen was stark.
But here, Hamilton struggled for pace, spinning during the morning practice session, before qualifying behind Bottas for the second time in as many races. But he was edged out by Vettel as the German took pole by less than a tenth of a second. Kimi Raikkonen (Ferrari) +9.637 4.
However, when the race-pace of Red Bull, Ferrari and Mercedes was compared this weekend, the difference in time was insignificant, with all signs showing that it will be another extremely competitive race.