Competition Commissioner Margrethe Vestager previously fined Google 2.4bn euros ($2.8 billion) over a separate probe into its shopping comparison service - a ruling Google is in the process of appealing against.
Small Google search competitors such as Qwant and DuckDuckGo said they now stand better chance of getting promoted by device makers.
- How much has Google been fined? In particular, Google has required manufacturers to pre-install the Google Search app and browser app (Chrome), as a condition for licensing Google's app store (the Play Store) and made payments to some equipment manufacturers and mobile network operators on condition that they exclusively pre-installed the Google Search app on their devices.
"The Commission's Android decision ignores the new breadth of choice and clear evidence about how people use their phones today", the Google CEO also wrote in a blog post the same day.
However, Google may challenge the ruling. "But with market dominance comes a responsibility".
The company was ordered by the European Commission on Wednesday to pay €4.34 billion ($5 billion) for unfairly pushing its apps on smartphone users and thwarting competitors. Pichai concludes by saying Google intends to appeal.
The case against Android is the most significant of three complaints by the European Union against the search titan, which has already been hit with a record-breaking 2.4-billion-euro fine in a Google shopping case.
"We will appeal the Commission's decision", he added. "A vibrant ecosystem, rapid innovation, and lower prices are classic hallmarks of robust competition", a spokesman for the company said.
He said the decision ignores the fact that "Android phones compete with iOS phones, something that 89 percent of respondents to the Commission's own market survey confirmed".
30 Nov 2010 - European Commission opens investigation into allegations that Google has abused its dominant position in online searches following 18 complaints.
2013 - Lobbying group FairSearch files a complaint about Google's Android business practices to the European Commission.
The penalty is almost double the previous record of 2.4 billion euros which Google was ordered to pay a year ago after its online shopping search service was deemed to be unfair to competitors.