The former Manchester United and Parma striker, who scored once against Catania and twice against Genoa before drawing a blank against Cagliari, made up for the absence of injured strike partner Mario Gomez with the second goal in a 2-0 win at the Stadio Atleti Azzurri d'Italia. Mati Fernandez had given Fiorentina the lead before the break.
The victory puts Vincenzo Montella's men back among the leading pack following last weekend's disappointing draw with Cagliari while stuttering Atalanta suffered a third defeat in four league games.
The quick feet and searing pace of Maxi Moralez would cause Fiorentina a lot of problems in the first half and in the ninth minute the Argentinian set up Daniele Baselli for a fierce shot against Stefan Savic.
Mario Yepes came close when teed up by Moralez but once again Montenegrin defender Savic saved the day with Neto beaten.
Fiorentina soon bared their teeth and Rafal Wolski skipped past Stefano Lucchini to force a firm punch from Andrea Consigli.
Neto blocked an attempt from former Viola midfielder Giulio Migliaccio before Fernandez saw a free-kick beat the Atalanta wall and shave paint off the crossbar.
Another Nerazzurro counter-attack found Carlos Carmona preparing to shoot at the far post, only for Nenad Tomovic to clear, and Fiorentina would survive the scare to open the scoring.
Four minutes before the break Borja Valero's delicious pass fell to Wolski, who was unfortunate only to hit the bar with his firm header, but Fernandez thought fast to tuck the rebound over the line.
Atalanta were perhaps right to feel aggrieved having dominated much of the half and they responded brightly following the restart, Davide Brivio missing the bar by inches with a bullet header.
Migliaccio then found it, with a little help from Neto, as the Fiorentina goalkeeper pushed an otherwise easy clearance onto the frame of the goal and out for a corner.
Consigli was given a wake-up call when Manuel Pasqual slipped the ball through to Joaquin for a first-time shot that clattered the stopper's feet.
Fiorentina kept up the pressure but when a classy pass from Massimo Ambrosini came into Rossi's feet in the box, the former Villarreal man could only clip wide.
His aim was truer in the 69th minute and this time it was Gonzalo Rodriguez who fed the diminutive frontman to notch his fifth goal in all competitions for Fiorentina.
Time was ticking rapidly away when Atalanta eventually came near to halving the deficit, German Denis testing Neto's reflexes with a snap-shot from a metre out, before Giacomo Bonaventura's right-footed drive whipped just wide of the mark.
The result was beyond Atalanta but they would enjoy the last solid chance of the game, Carmona's angled strike searing across Neto's goalmouth but out of play at the far post.