Movistar were 10 seconds clear of the field on the 11.6km stage, with Acqua and Sapone a further three seconds adrift.
That meant that Rodriguez saw his overall lead trimmed, but retained the yellow jersey with a seven-second cushion from Sergio Padrilla Bellon of Movistar.
Boosted by the time trial result, Movistar dominate the general classification, with David Lopez Garcia, Pablo Lastras Garica and Francisco Jose Ventoso Alberdi also featuring in the top six places.
"I’m quite happy," Katusha Director Mario Chiesa said, "we were able to keep the general classification leadership with our leader Joaquim Rodriguez gaining some seconds over one of the forerunners, Samuel Sanchez.
"We could have won today too: for some factors we didn’t, but it was a good performance anyways”.
The fourth stage of the five-stage event takes place on Saturday, with the riders navigating the 168km route from Roa de Duero to Ciudad Romana de Clunia.
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