The runaway championship leader, driving the apparently identical Red Bull, was a huge 2.5 seconds slower than his teammate Mark Webber in the first session at Valencia.
"There is a fairly simple explanation," team boss Christian Horner told the German broadcaster Sky.
"We were running different programs on the cars. We tried several different parts and got some good information.
"We are no longer allowed to test during the season so we only have a chance on Friday to try some things, particularly the first session," added Horner.
He would not specifically confirm that the parts tested by Vettel in P1 were related to the Silverstone spec exhaust and diffuser, admitting it is "impossible" to know what impact the FIA's clamp down will have.
"We know what benefit we get but not what benefits the others get. In reality the same teams will probably be at the front, but until Silverstone it's not possible to predict," added Horner.