Lando Norris took tenth on the grid after McLaren seemed to struggle compared to previous qualifying sessions.
The Mexican had returned a positive result from a Covid-19 test overnight Thursday and missed a second successive race, allowing Hulkenberg to impress again.
Unsurprisingly, when it mattered most, Hamilton turned up the wick with an impressive 1m25.2s to be a tenth clear of Bottas after the first run.
He said Mercedes felt they were "victims" and had been mistreated in the talks that had not been fair - allowing Ferrari to continue to hold a veto on the sport's rules and collect extra revenue for their historic standing.
"The mentality is to try to win it - that's it", he said.
"Valtteri did a good job and deserved the pole". The first race in 1950 was at Silverstone.
Assessing his last-gasp push on his final hot lap, Bottas said: "It feels good". So, we're struggling with getting them to last, but at the same time I think we got a good understanding of the balance. His teammate Lance Stroll only managed P8.
The second 90-minute practice session gets under way at 3pm.
He clocked a fastest lap of 1min 25.154sec to beat Hamilton by only 0.063 in the final moments of an enthralling qualifying session.
Team-mate Carlos Sainz, who will replace Vettel at Ferrari in 2021, finished 13th with Norris 4-1 up on the Spaniard in qualifying trim this term.
AlphaTauri's Daniil Kvyat was the shock casualty at this point, as he lost one lap to exceeding track limits and then ran wide at Becketts and damaged his floor.
Six times world champion Hamilton, victor of the British Grand Prix from pole position at the same circuit last weekend and 30 points clear of Bottas after four races without spectators, was 0.138 seconds slower.
Williams drivers Russell and Latifi finished the session in a respectable P15 and P16, whilst the bottom three consisted of Raikkonen, Kubica - who is driving for Alfa Romeo just in FP1 - and finally Magnussen.