Fiorentina were dominant from the off, as Antonin Barak and Cabral both had low efforts from outside the box well saved.
Marco Sportiello then displayed terrific reactions to deny Nicolas Gonzalez from point-blank range, somehow getting his body in the way of the ball after the forward flicked on a header from inside the six-yard box.
No matter how hard they tried, though, Fiorentina, looking to extend a run of 13 games without defeat, could not break the deadlock.
That left them susceptible to a sucker punch at the other end, and the Stadio Artemio Franchi was silenced when Atalanta took a shock 37th-minute lead with just their second shot of the game as Joakim Maehle burst into the box and converted past Pietro Terracciano.
Gonzalez had a glorious chance to level straight after the break before Gaetano Castrovilli lashed harmlessly off-target from inside the box.
The Viola were then gifted an opportunity to equalise when Toloi was ridiculously punished for heading the ball into his own hand inside the box, with the spot-kick duly dispatched by Cabral.
Atalanta were aggrieved, while Fiorentina had the momentum and they nearly took the lead for the first time when Cristiano Biraghi rattled the woodwork with a free-kick just seconds after coming off the bench.
Besides that, there was only one other clear-cut chance in a fragmented final 20 minutes, when Sportiello brilliantly dived low to his right to deny Giacomo Bonaventura in injury time.
The result leaves Vincenzo Italiano’s side seven points off the top six, while Atalanta have won just two of their last eight away fixtures.
Flashscore Man of the Match: Nicolas Gonzalez (Fiorentina)
