Caltrans finished the demolition project a year ahead of schedule, removing 11 piers this year.
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CHP officials had closed the Bay Bridge to traffic as a precaution, causing backups in both directions.
Sunday marks 81 years since the bridge first opened.
Piers E17 and E18, the last two piers, were successfully demolished this morning at 7:30 a.m., a spokesman said.
"It went well, it went according to plan," said Alejandro Lopez of Caltrans.
There was one minor hitch caused by a seal, Lopez said.
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"We had a slight delay because the seal was spotted in the exclusion zone," Lopez said. "We had marine mammal watchers on scene. We followed protocol, and after the animal left the area, we were able to successfully complete the implosion at 7:30 a.m."
The series of implosions to demolish the 1936 concrete structures took place over six weekends this fall, starting in September.
Caltrans combined multiple piers on certain demolition dates, allowing the demolition work to be completed a year ahead of schedule, saving taxpayers nearly $10 million, the agency said.
There was a traffic break on the bridge this morning to accommodate the implosion, but traffic quickly returned to normal after the implosion, Lopez said.