It looked as if Dons, the League One club who play such enterprising football, were going to cause an upset when Dean Bowditch deservedly fired them ahead.
The majority of the 19,506 record crowd were celebrating but Iceland's Helguson pounced on a defensive mix-up in the final minute of the match to earn a replay back at Loftus Road on January 17.
That was tough on MK Dons who played all the football, created the most chances and looked anything but 31 places below QPR on the footballing ladder.
MK Dons boss Karl Robinson is the youngest manager in the Football League, a passionate one too as he proved on Monday when he was sent off for an altercation with the referee during his side's win against Colchester, an incident for which he claims he will accept whatever punishment comes his way from the Football Association.
His team, however, have gained a reputation for free-flowing football and are many people's favourites to gain promotion to the Championship later this season.
They showed exactly why, particularly in a first half in which they punched holes in a QPR defence missing Anton Ferdinand and Paddy Kenny.
True, QPR might have taken the lead after two minutes when the MK Dons defence struggled to control a bobbling ball in the penalty area and DJ Campbell almost latched on to the opportunity but instead saw his would-be kick connect with fresh air.
But it was the Dons who settled to their pleasing rhythm quickest with Darren Potter and Stephen Gleeson creative in midfield and Luke Chadwick a constant threat up front.
Chadwick made 25 league appearances for Manchester United, scoring two goals, before being let go by Sir Alex Ferguson. But Old Trafford fans will remember his pace and his ability to excite and after nine minutes his bobbling shot found its way into the QPR net only for Jabo Ibehre to be ruled offside.
The League One side were swifter to the ball, more imaginative in their approach play and Chadwick should have done better after 21 minutes when Ibehre broke clear and outstripped the QPR defence.
He slid the ball inside to Chadwick, who had made a fine run from deep, and it seemed he must score but his tame right-foot shot was gathered easily by goalkeeper Redek Cerny.
Cup shocks rest on such incidents. There was another such moment when home fans believed their side should have had a penalty, QPR defender Clint Hill appearing to handle the ball in the box from a cross by Daniel Powell but referee Michael Oliver waved away the appeals.
QPR had the occasional foray and Campbell prodded the ball into the Dons net but was ruled offside.
Campbell then proceeded to miss the easiest chance of the match after 53 minutes. This time Federico Macheda, on loan from Manchester United, stole down the left flank and delivered a wonderful left-foot cross which evaded Dons goalkeeper Martin, only for Campbell to send his far-post header wide of the post from point-blank range.
It prompted QPR boss Neil Warnock to send on Helguson for Campbell on the hour mark
It was MK Dons, however, who opened the scoring three minutes later.
Shaun Williams crossed from the right and Helguson got into a tangle in the area, allowing Bowditch to dispossess him and send a left-foot strike past Redek Cerny into the net. It was no more than MK Dons deserved.
QPR suffered something of a late blow when Alejandro Faurlin was taken off on a stretcher with what appeared a serious leg injury after receiving lengthy treatment after 83 minutes.
Perhaps the delay upset the Dons. Whatever, there was a sting in the tail with Helguson cashing in on a mix-up in the MK Dons defence to slide the ball home for the equaliser after 88 minutes and earn a replay which both sides could have done without.
