The visitors refused to concede defeat and came within a couple of feet of stealing a dramatic victory, but Flood's late penalty landed just short before the fly-half saw a drop-goal charged down in the dying seconds.
An error-strewn encounter was marred by head injuries to Kelly Brown and Ugo Monye, who were both taken off after colliding as Scotland launched an assault on the England line, although initial reports suggest they were not as badly injured as first appeared.
When the hosts controlled the first half it looked as though Scotland coach Andy Robinson, sacked as England boss in 2006, was set for sweet revenge over his former employers.
But England improved, albeit marginally, after the break and it was enough for them to avoid what would have been a third defeat in a row at Murrayfield, although they have to go back to 2004 to find the last time they scored a try at the home of Scottish rugby.
The hosts started with plenty of vim and vigour and took the lead when young England prop Dan Cole was penalised for not releasing in the tackle, Parks marking his 50th cap with a simple penalty to get the scoreboard ticking over.
Johnson demands 'slicker' England
England also looked keen to put the ball through the hands and, after a couple of promising moves had broken down, they drew level when Wilkinson ignored the jeers to level the scores after 15 minutes.
As the half wore on Scotland started to monopolise possession and, when England conceded their third penalty in quick succession, Parks edged the hosts back in front.
Wilkinson levelled matters once again on the half hour mark, with the kick taking him past Ronan O'Gara as the all time leading points scorer in the championship with a new mark of 523 points.
But Parks finally succeeded with his third drop-goal attempt of the half to give the hosts a 9-6 lead at the break.
Despite attempts at adventure, primarily from Scotland, it had been a scrappy first half, with the scrums once again proving a major frustration as the front rows collapsed to the ground with great regularity.
England had been reduced to doing little more than defending for the first 40 minutes and when they did create a three on one chance, Wilkinson had thrown a wild pass into touch.
The fly-half managed to level the scores for a third time soon after the restart but it was his final contribution as he was injured making a tackle and was replaced by Flood.
Scotland should have won - Robinson
England had upped their game since the restart and Flood soon nudged them ahead for the first time in the game, but a Parks penalty rapidly levelled matters once again.
It was nip and tuck and looked increasingly as though one error - or a rare moment of inspiration - would settle the game.
A sickening collision saw both Brown and Monye taken off after suffering head injuries and with Parks hitting the post with a penalty and Flood pushing a similar effort wide the two sides were locked together entering the final quarter.
A sustained England attack ended with Flood putting the visitors back in front only for Parks, minutes after he hit the post for the second time, to level the scores yet again.
By now despite the less than stellar quality on show Murrayfield had turned into a cauldron, with every home attack greeted by thunderous noise from the stands.
England had a couple of late chances to steal the game but Flood's long-range penalty just lacked the legs, before Rory Lawson just got hands to the Leicester player's attempted drop-goal.
The ferocity of both sides' commitment was beyond doubt but neither was able to create much in the way of clear-cut chances and a draw was a fitting result.
Scotland: Southwell; S Lamont, De Luca, Morrison, M Evans; Parks, Cusiter; Jacobsen, Ford, Murray, Hamilton, Kellock, Brown, Barclay, Beattie.
Replacements: Danielli for Southwell (69), Godman for Parks (71), R Lawson for Cusiter (60), Cross for Jacobsen (71), S Lawson for Ford (65), Hines for Hamilton (51), MacDonald for Brown (55).
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.