Unbeaten Inter had conceded only one goal in their opening four Serie A games but fell apart against Zdenek Zeman’s team, who had been bottom of the table with only one point, after Yuto Nagatomo was sent off in the 28th minute.
Napoli eased the pressure on beleaguered coach Rafael Benitez with a 1-0 win at Sassuolo, ending a run of three Serie A games without a win, and AC Milan were held 1-1 at promoted Cesena.
Marco Sau pounced on poor defending by Nagatomo to head Cagliari in front in the 10th minute and, although Pablo Daniel Osvaldo replied for Inter eight minutes later, their troubles were only just beginning.
One minute after Nagatomo's sending-off, the Inter defence was slow to react after Samir Handanovic saved Daniele Dessena’s shot and Ekdal put Cagliari back in front.
The Swede scored again five minutes later, providing the finishing touch to Victor Ibarbo's run, and completed his hat-trick one minute before halftime after Inter's shambolic defence failed to clear a corner.
Cagliari, who moved up to 13th in the league, even missed a penalty in between when Andrea Cossu's effort was stopped by Samir Handanovic.
Napoli's performance still fell short of the level expected from a team who were seen as title challengers before the season.
Spanish forward Jose Callejon turned in Gonzalo Higuain's cross from close range just before the half hour to end Napoli's run of three Serie A games without a win.
After enjoying the best of the first half, Napoli were under pressure after the break against opponents who have only scored once in five games.
Simone Missiroli’s shot curled just over the bar on the hour and Napoli goalkeeper Rafael had an even bigger let-off when Federico Peluso's shot was deflected onto the bar by Juan Camilo Zuniga hear the end.
Napoli, third last season, have seven points from their first five games, already eight behind leaders Juventus and AS Roma. Argentina forward Higuain has yet to score a Serie A goal this season.
Milan, who also have seven points, fell behind to a Davide Succi goal in the tenth minute at Cagliari before Adil Rami headed the equaliser nine minutes later.
Milan defender Cristian Zapata was sent off in the second half for fouling Gregoire Defrel as he steamed towards goal.
(Writing by Brian Homewood in Berne, editing by Alan Baldwin)
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