Apple is punishing its rival for breaking its developers' policy, and comes a day after it took the same action against Facebook.
The move came after both firms used special access for market research.
“We’re working with Apple to fix a temporary disruption to some of our corporate iOS app,” Google said.
After more than 24 hours of disruption, Facebook had its access restored on Thursday.
"We are in the process of getting our internal apps up and running" a spokeswoman told the BBC. "To be clear, this didn't have an impact on our consumer-facing services."
Apple allows companies the ability to exert special control over employee devices in order to add additional security and control.
Many firms use this to distribute apps that might contain private information to employees but not the wider public.
Some firms also distribute test or beta versions of apps the firm is working on such as, in Google’s case, Maps, Hangouts and Gmail.
Both firms use internal iOS apps to help employees access services such as travel.
However, Apple explicitly prohibits firms from using this access on regular consumers.
On Monday it was revealed that Facebook had used its enterprise access to distribute a market research app to the public, including teenagers.
On Tuesday it became known that Google was doing something similar with its own app, Screenwise.
Apple appears to have stood firm on its position that "any developer using their enterprise certificates to distribute apps to consumers will have their certificates revoked”.
While Google has its own operating system, Android, a large number of the company’s almost 100,000 employees use iPhones for their work, and the firm releases much of its software on both Android and Apple’s iOS.
The row has been seen as a major escalation between Apple and its major rivals over protecting user data.