The English Championship winners were facing seven charges from a regulatory commission relating to the transfer and contract renewal of Argentine midfielder Alejandro Faurlin but were cleared on five of them.
"Although two of the charges have been found to be proved there will be no points deduction made from Queens Park Rangers in this season or the next," the FA said in a statement on their website.
The club was fined £800,000 pounds for breaching a rule E3 on "misconduct" and a further £75,000 for breaching agent regulations.
QPR's majority shareholder Bernie Ecclestone welcomed the decision that confirmed the club as champions.
"It would have been terrible if it had been anything else," Ecclestone told Reuters at the Turkish Formula One Grand Prix in Istanbul.
"It wouldn't have been fair. So I think they've acted correctly."
The Formula One supremo ducked questions about future investment in the club.
"I am the majority shareholder so I will decide what I want to do," he said.
Although QPR lost their final game 2-1 at home to Leeds United on Saturday they finished top of the standings on 88 points to secure a return to the Premier League for the first time since 1996.
"The lads have been through absolute agony over the last six weeks and how they've coped has been amazing," Rangers manager Neil Warnock told the BBC.
"I think we might celebrate tonight. It's probably the best moment in my career."
Norwich City finished second to also secure automatic promotion.
Swansea City beat Sheffield United 4-0 to snatch third place and a play-off semi-final against Nottingham Forest, who secured the final berth with a 3-0 win at Crystal Palace.
Cardiff City will play Reading in the other two-legged playoff with the play-off final on 30 May.
