Inter were rarely at their best in a game which simmered without ever sizzling, but Eto'o's individual brilliance and a couple of excellent saves from Julio Cesar were enough to separate the sides.
The game started off on a sour note, halted almost as soon as it had begun as racist chants believed to be directed at Eto'o rang out. The referee stopped the play and a public announcement was made asking fans to stop the chants.
After three minutes play resumed, and it was the home side who looked the sharper, though chances were hard to come by for both teams.
Maicon and Dejan Stankovic both tried shots from range for the visitors, but it was the hosts who came closest to breaking the deadlock when Andrea Cossu's crisp drive missed narrowly wide after excellent build-up from Francesco Pisano and Alessandro Agostini.
But the Cameroonian's sixth goal of the season came just six minutes before the interval - a rasping left-footed shot from twenty yards after turning past Davide Astori.
Maicon might have made it a two-goal lead at the break had he made firmer contact with Wesley Sneijder's cross.
After the break the game threatened to burst into life as the two sides played end-to-end football.
Cagliari, searching for an equaliser, went close after a Cossu's classy chipped through ball released Nene for a shot which Julio Cesar parried. The rebound fell to Alessandro Matri, but once more the Inter keeper stood up to the shot.
Eto'o remained a threat at the other end and Stankovic wasted an excellent opportunity by blazing a header over just after the hour.
The game quietened again, although there was time for Cagliari to go close once again with a quarter of an hour remaining.
A deflected Matri cross caught the crossbar and bounced towards Daniele Conti, but his effort at full stretch was smothered by Julio Cesar.
The clock ran down and Inter held on to record an important away win which takes Benitez's side top of the table - though Lazio have a chance to leapfrog them in the evening game.
Cagliari remain in the lower half of the table, but they may be more concerned about the possible consequences of the chanting which marred the game.