After Movistar had won the second stage by just two seconds from BMC, Rojas had little time to celebrate earning the leader's jersey in the one-week race before being hit with a three-minute penalty from race judges.
The controversy meant the overall lead was passed instead to his Movistar team mate and one of the race favourites, Alejandro Valverde.
The drama began after two teams, BMC and Trek-Segafredo, both complained about how Rojas had given team mates a helping push on an uphill stretch of the course.
"We have seen the pictures on the TV and they show clearly that Rojas pushes the other riders, which is forbidden during a race," UCI commissaries president Ernesto Maggioni told reporters.
"Every time he pushes, he gets a minute's penalty and a fine.
"Rojas was pushing. He was the last in the line and his team-mates are dropping back and he pushes them to take his place in the line because he was on the edge. That is forbidden."
Nelson Oliveira was also given a one-minute punishment and Andrei Amador a two-minute penalty for being given a helping shove by their team mate, who had already enjoyed podium celebrations and television interviews before the race judges investigated.
Rojas and the team had clocked a time of 48 minutes 55 seconds over the 41.3km course, with BMC Racing just behind and Chris Froome and his Team Sky colleagues third, 46 seconds adrift of Movistar.
At 41.3 kilometres from Pla de l'Estany to Banyoles, it was the longest time trial at this race since 1963, with both rain and a technical finish complicating life for the riders, including Alberto Contador, whose Trek-Segafredo team finished one minute 15 seconds behind Valverde.
"The truth is I am content, we gave everything," Contador said. "We were quite organised and I think we had a good time trial.
"We did finish far behind our direct rivals -- one minute 15 seconds behind Valverde is a lot of time."
The 36-year-old former Tour of Spain winner Valverde now looks favourite to win the race as it enters the Pyrenees on Wednesday with a 188.3km stage from Mataro to La Molina featuring three ascents.
(Writing by Rik Sharma; Editing by Ian Chadband)
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