Rangers lie 17th in the table, just one point and one place clear of the bottom three, having won just five of their 20 top-flight games this season.
Warnock, who led them to the Championship title last season, has now been removed from the post, with former Fulham boss Mark Hughes strongly linked with the new vacancy at Loftus Road.
The decision has been heavily criticised by many supporters, however, and Fernandes was forced onto the defensive.
The Malaysian businessman, a prolific user of social networking site Twitter, responded to many comments by insisting the decision was not a "knee-jerk" reaction to the team's poor recent form.
One such Tweet said: "Easy to call me an idiot. But its harder to make decisions. (It) may be the wrong one and ill be the idiot and ill go but at least ill stand up and be counted."
In another, Fernandes - who did receive messages of support as well - said: "Thank you. I apologise to the fans I have upset by this decision and I thank all of those who are keeping the faith."
Another said: "Not expecting all to be pleased but as a leader I have to make decisions. Indecision will kill everything. Time will tell if its the right decision."
Earlier, a club statement said: "Queens Park Rangers Football Club has today parted company with manager Neil Warnock.
"The board's commitment to retaining our Premier League status ultimately led to this decision. QPR assistant manager Mick Jones and first-team coach Keith Curle have also left the club."
Fernandes, who took over in the summer, said: "This decision has been made in the best interests of the club and I can assure everyone that this is not a decision that was made lightly.
"Sadly, our recent run of poor form has seen us slip alarmingly down the table and the board felt it was the right time to make a change.
"Neil has acted with honesty, professionalism and integrity throughout his time at the club, and I would personally like to thank him for his significant contribution to QPR over the last 22 months.
"I genuinely wish him all the very best for the future and he will always be welcome back at Loftus Road."
Warnock insists he leaves Loftus Road with his head held high.
"Obviously I'm very disappointed, but having achieved so much, I leave the club with a great sense of pride," he said.
"I have enjoyed my time here more than anywhere else and the QPR fans have been brilliant with me - they deserve success.
"My biggest regret is that the takeover didn't happen earlier, because that would have given me the opportunity to bring in the targets I'd pinpointed all last summer and probably given us a better chance to succeed in the Premier League.
"The board at QPR are hugely ambitious and I wish them every success for the future.
"I've been involved in the game a long time and I will be spending the immediate future with my family and friends before deciding my next career move."
The club statement revealed a further announcement on the recruitment of Warnock's successor will be made "in due course".
Chief executive Philip Beard acknowledged they are under pressure to make an appointment to enable them to reinforce their squad this month.
He said on Sky Sports News. ""I'm not going to comment (on candidates) tonight but what I will say is that we're going to move as quickly as we can and we hope to make an appointment very soon.
"Time is against everybody and we're already into the second week of January. I think the reality is there are some funds there but we've got to make the right purchases."