Jonathan Tuffey saved a Giampaolo Pazzini penalty but Sergio Pellissier added the third 18 minutes from time.
Daniele Mannini grabbed a brace and Giampaolo Pazzini and Reto Ziegler scored the others in Samp's win.
CNN: Real Madrid held goalless in Spain; Inter stay top in Serie A
Meanwhile in Serie A, Giampaolo Pazzini scored twice as AC Milan overran 10-man Lazio 3-0 at the San Siro on Saturday.
Balotelli will be suspended now against Napoli and Giampaolo Pazzini will play.
Galatasaray's Morgan De Sanctis will probably get the nod in goal and Catania's Giuseppe Mascara could join Giuseppe Rossi and Giampaolo Pazzini in attack.
Meanwhile Defence Minister Giampaolo Di Paola said he would not step down over the crisis because he did not want to "abandon a ship in difficulty".
Meanwhile, ahead of the new season a major transfer switch was completed Wednesday with AC Milan and Inter agreeing to swap strikers Giampaolo Pazzini and Antonio Cassano.
Elsewhere, AC Milan claimed a 2-1 win over Siena thanks to goals from Bojan and Giampaolo Pazzini, while there were also wins for Chievo, Genoa and Parma.
After Iaquinta wasted a defence-splitting De Rossi pass in the 60th minute, Lippi again made a further change with in-form Sampdoria striker Giampaolo Pazzini replacing the ineffective Claudio Marchisio.
The struggling visitors took a seventh-minute lead through Sergio Floccari but goals later in the first half from Stefano Guberti and Giampaolo Pazzini were enough to give Samp the three points.
CNN: Inter held by Genoa in San Siro but stay four points clear
Prosecutors in Bari are investigating a businessman, Giampaolo Tarantini, who claims to have sent 30 women to parties at the prime minister's residence in Rome and paid some to stay the night.
ECONOMIST: Silvio Berlusconi under fire: The sultan and the vizier | The
That so many flowed through this pipeline from semi-obscurity in Spain and Italy to the semi-obscurity of a suburb northwest of London is no coincidence: All three clubs belong to Giampaolo Pozzo, a longtime owner in Italy.
One involves claims that he was blackmailed by Giampaolo Tarantini, a businessman from the southern city of Bari who is alleged to have supplied more than 100 women, including numerous prostitutes, for parties at Mr Berlusconi's homes.
Indeed, Milan has had a whole range of players stepping up in turn, like centerforward Giampaolo Pazzini, who earlier this season went 11 games without scoring, but on Saturday notched two of the three goals that sank Lazio, allowing Milan to leapfrog its opponent into third place.
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