Miguel Indurain, who is extremely keen to win his home tour, also moved into contention with his third-place finish on the 10th stage, but Rominger's triumph in the 28.75-mile test served only as consolation, as he dropped more than seven minutes on the leaders in the fourth stage.
With 12 stages remaining, the fight for the title seems to be between Zulle, Indurain, third-placed Laurent Jalabert and the 1991 winner, Melchor Mauri, in fourth.
"For me, the Vuelta is already lost," Rominger said, after beating Zulle by two seconds. Indurain finished a further 25 seconds back.
In the overall standings, Zulle leads Indurain by 1min 04sec and Jalabert by 1:15.
"Alex is a great rider, it will be difficult to catch him," Indurain said. "It was one of the strangest time-trials of my career. The wind hit from all sides - I didn't like it at all."
Jalabert, who ensured his 1995 Tour victory in Avila, was out of luck this time after being hampered by a puncture on the city's cobbled streets. The Frenchman was fifth, 1:52 behind Rominger, and just two behind Mauri of Spain. Zulle, Mauri, Jalabert and the fifth-placed Australian rider, Neil Stephens, all ride for Spain's ONCE team.
The trial took its toll on Italian sprinters Fabio Baldato and Giovanni Lombardi, who had been first and second overall, and they dropped out of contention.
The Tour continues today with the 123-mile 11th stage from Avila to Salamanca.Reuse content