A first-half goal from Brazilian international Igor Jesus proved the difference as Botafogo all but sealed a place in the knockout rounds at the Pasadena Rose Bowl.
French champions PSG are widely regarded as one of the favourites for FIFA's 32-team tournament after a dazzling season which culminated with a scintillating 5-0 demolition of Inter Milan in the Champions League final last month.
But their hopes of securing a victory which would have seen them become the first side to reach the last 16 were stymied by a resilient performance from their opponents from Rio de Janeiro.
Paris Saint-Germain picked up where they had left off in Sunday's 4-0 Group B rout of Atletico Madrid, with Khvicha Kvaratskhelia testing Botafogo goalkeeper John with an early curling effort after just two minutes.
But that early effort was as close as PSG came to scoring in a scrappy first half punctuated by a series of niggling fouls that prevented the European champions from settling into their passing game.
Botafogo's midfield trio of Marlon Freitas, Gregore and Allan worked tirelessly to close down Vitinha, denying the skillful PSG playmaker time and space to launch attacks despite dominating possession.
Instead, it was Botafogo who took the lead with a goal against the run of play on 36 minutes.
Jefferson Savarino's perfectly weighted through ball split the PSG defence and sent Jesus racing through on goal.
The Botafogo striker did brilliantly to wrongfoot the covering Willian Pacho before sweeping a shot that took a slight deflection past PSG goalkeeper Gianluigi Donnarumma on its way into the net.
PSG continued to dominate possession through the second half, and spent long periods camped in the final third.
But Botafogo's defence held firm and the result leaves the Brazilians firmly on course for the last 16, with a final group game against Atletico Madrid to come in Pasadena on Monday.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)