Defender Pinnock celebrated signing a new four-year contract earlier in the day by scoring an 85th-minute winner to snatch a 1-0 victory for the Bees.
With the title long since sewn up, Pep Guardiola rested some of his big hitters ahead of next weekend's FA Cup final, and a potentially historic Champions League showpiece seven days later.
With Kevin De Bruyne and Jack Grealish missing completely and Erling Haaland left on the bench, it was a scratch City side and those established stars who did play, like Phil Foden and Riyad Mahrez, had little impact.
Brentford still had something to play for, by contrast, as they were in with a slim chance of qualifying for the Europa Conference League before wins for Tottenham and Aston Villa ultimately scuppered their hopes.
Their players applauded the champions onto the pitch, but that was as far as the respect stretched.
The Bees may still be adjusting to life without suspended striker Ivan Toney but they remain a potent threat, with Yoane Wissa beating Emerson with a curler against the far post before an offside flag was raised.
Brentford goalkeeper David Raya, who looks destined to leave the club this summer, had to make an early diving save to deny Cole Palmer before Kalvin Phillips, getting another run-out in a midfield three alongside Palmer and Rico Lewis, sent a low shot wide.
Emerson saved well from Vitaly Janelt's snap-shot at a corner as Brentford pressed, and the German midfielder lifted another effort over the crossbar.
After the break Brentford, who won at the Etihad in November, felt they should have had a penalty after Lewis slid in on Ben Mee.
But referee John Brooks waved away the appeals - with VAR agreeing - and then booked Bees head coach Thomas Frank for his protests.
By now City well and truly had their eye on the bigger battles to come, but the Bees kept driving forward and Frank Onyekas drive flew over before Bryan Mbeumo just failed to get a touch on to Janelts chip into the area.
The winner came from a cross by substitute Kevin Schade which was headed back across goal by Mbeumo and emphatically finished by Pinnock.
City briefly woke up and Raya somehow denied Palmer an equaliser from close range.
Defeat meant City did not break the 90-point mark for a record fourth time in the Premier League, which will irritate Guardiola, but if they win their next two matches - at Wembley and in Istanbul - even the perfectionist will have forgotten that.