Murray went into the match with a 4-1 career record against Del Potro, but the 21-year-old Argentine has moved up the rankings to fifth in the world this season and - unlike Murray - has already won a Grand Slam title.
Cilic dropped the first set but took a 2-1 lead as Del Potro struggled to find his top form.
Ferrer's victory means that Federer faces world No. 3 Andy Murray on Sunday in a rematch of the Wimbledon and Olympic finals, while Del Potro plays No. 1 Djokovic -- who won all three of his Group A games.
Del Potro broke Federer to level at 1-1 in the second, but the Swiss cruised to victory to the Basle crowd's delight.
In Serie A, Juventus went back on top as Alessandro Del Piero scored the winner in a 2-1 win over Lazio in Turin.
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El Times de hoy, por ejemplo, apenas toca las alternativas de la victoria del West Ham sobre el Arsenal (1-0) , a pesar de su gran importancia.
Barcelona's Mundo Deportivo newspaper screamed, "No Excuses, " on its front page after the 3-1 humbling against Real in the Copa del Rey.
New York paid for a penalty early in the first period after defenseman Michael Del Zotto went to the box for cross-checking at 1:46.
Britain's Andy Murray , the sixth seed, beat Switzerland's Stanislas Wawrinka 6-1 6-3 6-3, and will next play Argentina's Juan Martin del Potro , who defeated Kei Nishikori of Japan 6-3 6-4 6-3.
The 20-year-old Argentinean took the Swiss world No. 1 to five sets, including two tiebreakers that went Del Potro's way, winning 3-6 7-6 (7-5) 4-6 7-6 (7-4) 6-2.
"The game last night meant nothing if we didn't follow up with two points again tonight, " Del Zotto said, referring to New York's 2-1 shootout win over Carolina on Monday.
In Spain , Real Madrid booked its place in the last four of the Copa del Rey, despite being reduced to nine men during the 1-1 draw at Valencia.
The Spaniard will next play either world No. 1 Novak Djokovic or Juan Martin del Potro, who eliminated third-ranked Andy Murray on Friday.
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Spain international Casillas has not played for Real since being injured in January, but in his absence the reigning Spanish champions have been on a fine run, beating Barcelona in the semifinals of the Copa del Rey and in their 'El Clasico league clash Saturday, winning 2-1.
Del Potro, the 2009 U.S. Open champion, eventually triumphed 1-6 6-4 6-3 in just over two hours and will now face either Canada's Milos Raonic or Jarko Niemenen, from Finland.
He will next take on either Czech seventh seed Tomas Berdych or 2009 U.S. Open champion Juan Martin del Potro of Argentina -- who led 7-6 (8-6) 1-6 6-3 when play was halted long before the Tsonga-Wawrinka match, despite appearing to struggle with a strapped-up knee.
It set up a final with Serbian No.1 Novak Djokovic, who beat Juan Martin del Potro of Argentina, 6-3 7-6 in the earlier last four clash.
Alvaro Negredo, who had played just 30 minutes at the tournament as a substitute in Spain's 1-0 group-stage win over Croatia, did little to justify Del Bosque's surprise decision to name him to the starting lineup.
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Leading 2-1 from the first leg, Juve edged further ahead when veteran striker Alessandro Del Piero scored on 28 minutes but Serie A leaders Milan hit back with goals from Djamel Mesbah and Maxi Lopez to force an extra half an hour.
Argentine Juan del Potro also won in four sets as he saw off Go Soeda 6-2 6-3 1-6 6-4 on Court 18.
Chardy will next face former U.S. Open champion Juan Martin Del Potro, the sixth seed who beat Serbian Viktor Troicki 7-6 2-6 6-1.
Murray's quarterfinal opponent will be Berlocq's compatriot Juan Martin del Potro after the 2009 U.S. Open winner breezed past veteran German Tommy Haas 6-1 6-2.
The Czechs, who are looking for a first win in the competition for 32 years, will take a 2-1 lead going into Sunday's deciding singles where Argentina will be without Juan Martin del Potro.
World No. 19 Juan Monaco, Argentina's No. 1 in the absence of Juan Martin del Potro, gave his country a lifeline by beating 13th-ranked Gilles Simon 7-6 (7-2) 6-2 6-4 on the red clay.
Meanwhile, former world No. 1 Rafael Nadal will make his long-awaited return to action at the Chile Open in Vina del Mar early next month.
"The minimum amount of warming predicted by scientists - 3 degrees Fahrenheit - should be increased by at least 1 F as a result of the new findings, " said Del Genio.
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