Hamilton's auto sustained significant damage in the incident, and he will now start Sunday's race, the penultimate grand prix of the season, from the back of the field.
With Lewis Hamilton out of qualifying following his crash in Q1, Bottas led the Silver Arrows' challenge for pole in Brazil.
TOP TEN: Valtteri Bottas (Mercedes), Sebastian Vettel (Ferrari), Kimi Raikkonen (Ferrari), Max Verstappen (Red Bull), Daniel Ricciardo (Red Bull), Sergio Perez (Force India), Fernando Alonso (McLaren), Nico Hulkenberg (Renault), Carlos Sainz (Renault), Felipe Massa (Williams).
The Mercedes-AMG Formula One team minibus was robbed at gunpoint outside the Brazilian Grand Prix circuit in Sao Paulo on Friday night when the team was returning back to their hotel. Bottas said the incident spurred him on to extract even more out of his performance and seal his third pole in F1. "We have a good vehicle and it's going to be a close race still with Ferrari but I'd rather start from pole than, for example, P3 so I'm looking forward to tomorrow".
"It was a pretty scary situation - it's not a very comfortable feeling, not great".
"The lap was fine [but] I knew I had a bit left".
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"It was a shame that Lewis is out, a shame for us, but I stood up for the team and it is good to start from pole position here". We have a good vehicle. "I'm looking forward to tomorrow".
Bottas was second, a fact that will frighten Vettel if the two drivers continue their scintillating form.
Due to his failure to set a laptime, Hamilton will start from the back of the grid for Sunday's race but the Briton is remaining positive - and takes heart from his drive through the field from P18 in 2009.
"It's always good to have a target, it makes you work harder and try harder".
Hartley finished nearly two seconds slower than Bottas in 17th place.
"I'm okay. It happened really quickly".