How to replace string only once without regex in Java?

You should use already tested and well documented libraries in favor of writing your own code!

StringUtils.replaceOnce("aba", "a", "")    = "ba"

The StringUtils class is from Apache Commons Lang3 package and can be imported in Maven like this:

<dependency>
    <groupId>org.apache.commons</groupId>
    <artifactId>commons-lang3</artifactId>
    <version>3.8.1</version>
</dependency>