Inter fell behind to Jeda's first-half penalty after Maicon had been adjudged to push over Alessandro Matri in the box.
Coach Jose Mourinho, later sent to the stands for arguing with officials, brought on forward Mario Balotelli at the break to change shape and the move paid dividends just as it had in the previous weekend's 2-0 win over Parma.
Good pressure by Samuel Eto'o forced the home defence to give the ball away and Argentina's Milito ran through to score on 51 minutes before dinking in a second five minutes later following a long ball over the top.
Milito, who signed for Inter in the transfer window following a successful spell last season at Genoa, took his tally to an impressive 28 goals in 35 Serie A appearances.
"It's great to score but what pleases me more is the joy of victory," he told Sky television. "It was tough both physically and mentally, we came up against a strong Cagliari side."
Inter, who drew 0-0 with Barcelona in the Champions League on Wednesday and host Napoli in midweek, are third on 10 points.
Leaders Juventus made it four wins from four in Saturday's 2-0 victory over Livorno and Sampdoria joined them at the top after securing maximum points from the first four games of the season for the first time with a 4-1 thrashing of Siena.
AS Roma overcame Fiorentina 3-1 to record their second league win in a row under new coach Claudio Ranieri.
Francesco Totti, criticised by Ranieri on Saturday for his lack of movement, converted a penalty before slamming in a second and then crossing for Daniele De Rossi to bury a header on 42 minutes. Alberto Gilardino netted a late consolation.
CLASSY GOAL
Clarence Seedorf, playing in place of 'flu victim Ronaldinho, netted a classy goal in the second half to hand Milan victory but visitors Bologna had chances to snatch a draw.
Seedorf won the ball on the edge of his own box and, despite Bologna appeals for a foul, he laid the ball off to Massimo Ambrosini and charged up field.
Ambrosini found the Dutchman with an intelligent pass and Seedorf cut through a weak defence to score from close range.
Substitute Filippo Inzaghi, who replaced the ineffective Klaas Jan Huntelaar, hit the post late on but the Rossoneri remain a work in progress after an inconsistent start.
Genoa, who like city rivals Samp were going for a fourth straight win, lost 3-1 at Chievo.
Julio Cruz grabbed a 1-1 draw for Lazio at Catania while promoted Parma beat coach Francesco Guidolin's former side Palermo 1-0. Atalanta stayed bottom with no points after a 4-1 loss at Bari.
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