Beckingham, 48, the former head of the Design Services group at Barrow Borough Council, was accused of failing to ensure the ageing air-conditioning system at a council-run arts centre in the Cumbrian town was properly maintained.
This fault allowed the deadly bug to breed and infect visitors, Preston Crown Court heard.
At least five people died and around 172 others were infected after the faulty system sprayed deadly bacteria into the air from the Forum 28 centre in summer 2002, the court heard.
But Beckingham, from Grange-over-Sands, Cumbria, denied the charges and was cleared by a jury of eight men and four women after a seven-week retrial.
However, she was fined £15,000 after being found guilty of one charge of breaching the Health and Safety at Work Act.
Beckingham wiped tears from her eyes as the not guilty manslaughter verdicts were read out. From the public gallery, survivors and the relatives of victims also wept.
The prosecution had alleged in court that Beckingham cancelled a contract which ensured necessary tests were carried out on the air-conditioning unit.
She was in charge of design services for the local authority but had received no health and safety training from her employer, Barrow Borough Council, the court heard.
The court also that heard she was on holiday when a second contract to maintain the air conditioning system was agreed with a subcontractor.
Beckingham told the court her job as senior architect at the council mainly concerned the design of local housing projects. The court also heard of failings in health and safety procedures throughout the local authority.