MILAN - Diego Milito scored his twentieth of the Serie A season, with Cristian Chivu and Mariga netting their first in black and blue as Inter went top of Serie A.
Atalanta made a fast start at the Stadio Giuseppe Meazza and the Nerazzurri were on the back foot in the fifth minute when Simone Tiribocchi scored.
But Inter soon seized control and took the lead after a devastating ten-minute spell, Milito lobbing the keeper and Mariga finishing off a well-worked move.
Any hopes of stay-up points for the relegation-threatened side were scuppered with twelve minutes left when Chivu gave Inter a two-goal cushion with a blistering long-range shot.
The win lifts José Mourinho's men above Roma, who take on Sampdoria in Genoa tomorrow night.
With next Wednesday's Champions League tie at Barcelona in mind, the Inter coach rotated numerous players against the Bergamo Nerazzurri.
African midfielders Mariga and Muntari started in a diamond midfield with Stankovic in the middle and Sneijder in support of front pair Milito and Eto'o.
Maicon, out of action after several trips to the dentist, was replaced at right-back by Zanetti, with Cordoba partnering Materazzi and Chivu filling the left-back slot.
It didn't take Atalanta long to get into their stride and Tiribocchi took full advantage of a defensive mistake, firing past Julio Cesar after latching on to Manfredini's through ball.
Inter were level on 24 minutes when Milito lobbed the stranded Coppola to punish a Bianco's moment of defensive suicide.
Mariga celebrated his 100th appearance in a European league with Inter's second goal ten minutes before half time. Sneijder attacked down the left and served Eto'o, who pulled back into the middle of the area for the Kenyan to fire in off Muntari.
Atalanta started the second half as they began the first and Guarente missed by a whisker, moments before Manfredini's rising drive produced a tipped save from Julio Cesar.
But Inter gradually wore their local rivals down and made sure of the points on 78 minutes when Chivu received from Eto'o and crashed a magnificent long-range shot beyond Coppola to stretch the Nerazzurri's long unbeaten home run in Serie A to 40 games.
Inter 3-1 Atalanta (HT: 2-1)
Scorers: Tiribocchi 5, Milito 24, Mariga 35, Chivu 78.
Inter: 12 Julio Cesar; 4 Zanetti, 2 Cordoba, 23 Materazzi, 26 Chivu; 17 Mariga, 5 Stankovic (8 Thiago Motta 70), 11 Muntari; 10 Sneijder (19 Cambiasso 46); 22 Milito (89 Arnautovic 80), 9 Eto'o.
Subs not used: 21 Orlandoni, 6 Lucio, 7 Quaresma, 25 Samuel.
Coach: José Mourinho.
Atalanta: 32 Coppola; 4 Capelli, 77 Bianco, 5 Manfredini, 13 Peluso; 79 Ferreira Pinto (9 Amoruso 57), 22 Padoin, 17 Guarente, 20 Valdes (70 Ceravolo 57); 72 Doni (21 Radovanovic 71), 90 Tiribocchi.
Subs not used: 91 Rossi, 6 Bellini, 15 De Ascentis, 19 Chevanton.
Coach: Bortolo Mutti.
Referee: Daniele Orsato (Schio).
Booked: Bianco 8, Stankovic 27, Cordoba 47, Manfredini 64, Coppola 64, Materazzi 83.