"The umpires had determined that the condition of the ball had been deliberately altered," match referee Steve Bernard said.
"Under the laws of cricket they imposed the five-run penalty against the Victorian side and replaced the ball."
Former South Australian and Australian players Greg Blewett and Jason Gillespie took to social media to slam Lewis after the incident.
"Very poor from anyone let alone a member of the support staff," Gillespie tweeted.
"Disgrace!" posted Blewett.
In 2005, current Victorian coach David Saker was cleared of any wrongdoing after an investigation into alleged ball tampering during a Second XI match did not uncover enough evidence. Saker had been coach of the team at the time.
Aaron Finch, who captained Victoria at times this summer, was fined with ball tampering while playing a Sheffield Shield match for the state in 2010.
It is the second time controversy has hit the match, after the Redbacks appealed for obstructing the field against Victorian Peter Handscomb on Sunday when he hit away a return throw to the wicketkeeper.
"I knew I was within my rights to hit the ball if it was coming at me," Handscomb said of the incident on Monday evening.
"So I wasn't too worried about what was going to happen."
- AAP