The Tinkoff-Saxo man finished fourth in the 36.7-kilometre 10th stage between Real Monasterio de Santa Maria de Veruela and Borja, with Omega Pharma-QuickStep's Tony Martin taking the honours with a time of 47 minutes and two seconds.
Martin's team-mate Rigoberto Uran was second, 15 seconds off the pace of the German, while Trek Factory Racing's Fabian Cancellara was third, a further three seconds slower.
The result means Contador now has a 27-second advantage over Movistar's Alejandro Valverde - eighth on Tuesday - but the two-time Vuelta champion is not getting too far ahead of himself with 11 stages still to come.
"I'm very pleased," the Spaniard said. "I'd never have thought this was possible when I started the Vuelta.
"To be honest, I'm racing this now without any pressure, I will take this day by day and the rest of what happens in this race is not yet clear.
"If I win it - great, but either way, I'm tremendously satisfied with what I've done so far.
"There's a long way to go, for sure, and in some ways the ideal thing would be to let the jersey go and then get it back in the time trial on the last day.
"It's good to lead, because you have the edge on your rivals, but I'm very conscious there is a long way to go before the finish. I remember the Dauphine, where I was leading on the last day and then the whole thing fell apart.
"The advantage, now, is that I can wait for my rivals to make a move. But we will have to see how my legs are feeling after a hard time trial like today's."