Inverdale caused a storm when listeners heard him say Marion Bartoli - who went on to be women's champion - was "not much of a looker".
Balding had previously been the station's Wimbledon host, but was unable to front the coverage due to other commitments.
Inverdale will continue to work on the BBC's tournament coverage with highlights on TV.
A spokeswoman for the station said: "We have a wide team of talent that work across TV and radio at Wimbledon and John is very much a part of this again this year, and will present the daily highlights pro-gramme on BBC2, Today At Wimbledon.
"Clare Balding reprises her presenting role on Radio 5 Live, which she has done before."
Inverdale told earlier this week how a bout of hay fever and efforts to fill airtime had been behind his comment.
The 56-year-old told Radio Times magazine: "I was feeling so ill that day, I had terrible hay fever and all I could think of was that I wanted to go home to bed.
"I had Andy Murray in the final the next day, I knew I had to be on form. Your mind is going all over the place, we're on air from 12 noon till 7pm with not a single word written and you've got to fill the time."