Sebastian Vettel faded to sixth for Ferrari, seven-tenths of a second off the lead time.
At the time of the robbery, Mercedes' world-championship winning team were returning back to their hotel after preparing for Sunday's Brazilian Grand Prix.
Sebastian Vettel was left ruing a mistake on his final hot lap in Formula 1 qualifying for the Brazilian Grand Prix after missing out on pole position by just 0.038 seconds.
The current F1 champione-elect tweeted that some of his crewmembers were, "held up at gun point" as the team minibus was leaving the Interlagos circuit in São Paulo on Friday night.
However, Hamilton is marking his fourth world title with a new helmet design this weekend, featuring the No.1 and a fourth star on both the side and the top.
Hamilton reacted to the incident on twitter and called on the FIA to review the safety procedures surrounding the event.
Hamilton has been the best qualifier of the season with ten pole positions and 12 front-row starts so far in 2017.
In a bid to avoid such issues, mechanics and team staff have been advised against wearing branded team clothing away from the circuit.
The 32-year-old Englishman remained in his cockpit for some moments before informing his team that he was not injured in the high-speed smash.
"I think I chickened out a bit on the brakes on the last lap going into Turn One", he said.
"I'm OK. It happened really quickly", Hamilton said.
"It's very unusual from me but it shows we are all human and things happen". Hamilton has raced with 44 since Formula One first introduced permanent driver numbers in 2014, choosing the double digit because it was the same one he raced with in go-karts.
"I will try to have as much fun as possible tomorrow".
"I tend to just look at it as challenges are what makes life interesting and overcoming them makes life meaningful".