Johnson rested from opening ODI with England
Australia's Mitchell Johnson (R) and Ryan Harris celebrate their 5-0 victory in the Ashes Test against England in Sydney on January 5, 2014
The lethal left-arm paceman was the star of Australia's 5-0 Ashes clean sweep of the tourists with his express bowling, finishing with 37 wickets at 13.97.
Johnson will miss Sunday's opening one-dayer in Melbourne but will return for the second match at the Gabba on January 17.
"It's obviously been a big summer for him so we will just give him a short break," Lehmann told reporters.
"It's about making sure he is fresh for the other one-dayers as well.
"It's important that we put out the best side we possibly can but we have to understand it's been a hectic five Test matches and some of the Test boys especially are getting a bit weary," Lehmann added.
"Mitch will play in Brisbane definitely. It's one of his home towns. We want them to play in their home state."
It is likely that Test stars Michael Clarke, Brad Haddin and Shane Watson could also be given matches off during the ODI series, the coach added.
The losing Ashes team from the past three series has bounced back to win the subsequent one-day tournament, including England in 2006-07 when they were also crushed 5-0 in the Test matches.
But Lehmann wants his team to continue England's winless tour.
He said Australia's victory against England in the ODI tournament that followed the 2013 Ashes defeat had helped lay the foundation for this southern summer's Ashes whitewash.
"England will be trying to do the same thing and they will be building for the World Cup," he said.
"We have got to keep the momentum going because winning becomes a habit."
Lehmann said strong performances in the five ODIs against England would count for something when selectors decide on the tour squad to head to South Africa on January 29.
"Every time you represent your country you're trying to play in all formats," he said.
"Every game is important for guys to make runs and take wickets."
Fast bowler James Pattinson is looking to make it back for the South Africa tour after missing the majority of the Australian Ashes series with stress fractures.
He is in line to join Ashes destroyers Johnson, Ryan Harris and Peter Siddle in South Africa, however Lehmann said the 23-year-old paceman needed to earn his recall.
"He needs to bowl well, like everyone else is playing, trying to get on that trip," he said.