Fernandes has made the decision two weeks on from QPR being fined £17m as part of a £42m settlement for breaching Financial Fair Player rules, which he believes leaves the West London outfit on more stable footing in the long term.
"It's a good time for a change as the club is now in a stable position and this will give the new chairman a good foundation to build upon," he told the club's official website.
"It's time for the club to have a chairman who is based in London. It was important for me to step down at a time where we have solved many issues such as FFP, making the club sustainable, building a strong academy and having a strong backroom team.
"I remain a committed shareholder and co-owner and will do what I can to get QPR back to the promised land."
Bhatia has been on the board at QPR since 2007.