However, James Lowes’s spirited side ignored their personal afflictions to push on and gain a dramatic win, staving off a tremendous amount of pressure to hold on at the death.
Indeed, Doncaster’s giant replacement prop Joe Sproston actually got over their goalline twice in injury-time. On the first occasion, he was clearly denied but with the second - which proved the last play - he was adamant he touched down.
Referee Greg MacDonald deliberated with his assistant, though, who ruled the front-row, having ignored a clear overlap to go himself with Carnegie down to 14 men after Elliot Millar-Mills’ yellow card, had not legitimately crossed.
Knights director of rugby Clive Griffiths was quietly seething afterwards about that decision although, as his side received penalty after penalty as they pressed hard in those closing stages, his opposite number could have pointed to missed calls that went against his own team during that breathless period, including one blatant Doncaster knock-on.
It is hard to argue the hosts did not deserve the points given the way they defended their line so stoutly during that spell and also having fought back from 9-3 down early in the second period.
Admittedly, it was mainly due to pure grit, desire and endeavour given there was little chance of much free-flowing rugby with heavy showers pouring down sporadically throughout the 80 minutes at Headingley.
Nevertheless, as second-half tries from Ollie Stedman and Jack Whetton saw them rally, it was an impressive reaction considering the problems they had faced.
Issues started even before kick-off when fly-half Alex Davies strained a hamstring in the warm-up, meaning a late call for former Harrogate No 10 Callum Irvine, to make his first Championship start.
Tighthead prop Charlie Beech was replaced after just 18 minutes due to a head injury and then Carnegie lost their captain Richard Mayhew, who hobbled off in agony with a foot problem before the half-time interval, later leaving the ground on crutches.
To make matters worse, his replacement Richard Beck suffered a hand injury early in the second period but Lowes’s side – six points adrift at that point – remained unperturbed.
Lowes admitted: “You’re always nervous when you roll a finish like that, but I am pleased for them.
“We missed three kicks, nine points, we should have taken so it was going to be more frantic at the end.
“There were a couple of penalties on their line we don’t need to give away either and they (Doncaster) had a go.
“But I want us to be a good defensive side and hard to beat and today we were. They have to work really hard for each other and they did that.”
After Simon Humberstone slotted his third penalty in the 44th minute, Doncaster faced plenty of pressure at the start of the second period and eventually succumbed.
Initially, Carnegie’s Millar-Mills spilled trying to trundle through and then the visitors drove through a scrum on their own 22 to earn a penalty.
However, they lost the resulting line-out to invite more pressure and, soon after, Lowes’s side scored via a rolling maul, ex-Doncaster No 8 Stedman coming up with the ball in the 57th minute.
Replacement scrum-half Will Homer took over kicking duties from Irvine, but he was unable to convert.
However, the 21-year-old, who is on a dual-registration deal from Bath, produced a classy moment soon after to put his side in front.
With virtually all his team-mates on the openside at a ruck 15m out, he pirouetted to go blind with only lock Whetton in support against a welter of Doncaster defence.
Nevertheless, a sharp acceleration and pass to the forward saw Whetton suddenly advancing to the corner for the simplest of tries.
Homer improved from wide out but he badly skewed a 40m penalty which meant unbeaten Doncaster - who had vanquished Rotherham Titans 44-0 previously and beaten Jersey - still had hope going into the final throes.
Knights had controlled the first period and, indeed, felt Tyson Lewis had crossed in the 17th minute following some slick passing from locks Matt Challinor and Tom Hicks only for the assistant referee to rule the winger had been forced into touch behind the goalline.
Challinor was sin-binned for a late tackle on Irvine but the fly-half was wayward with the 40m penalty and it was not until the 39th minute the hosts got off the mark.
However, they certainly made up for lost time in that second period and have now won their last two matches after the opening day loss at London Scottish.
Yorkshire Carnegie: Elder; Watkins, Forsyth, Lucock, H Davies; Irvine, Green (Homer 54); Thomas (Imiolek, Buckle (M Mayhew 54), Beech (Millar-Mills 28), Whetton, Smith, Bainbridge, R Mayhew (Beck 38-Myerscough 51), Stedman.
Doncaster Knights: Foley; J Bulumakau, A Bulumakau, Owen, Lewis; Humberstone (Cusack 67), Heaney (James 67); List (Bergmanas 62), Hunter (Nelson 60), Quigley (Sproston 62, Challinor (Eames 60), Hicks, Shaw, Hills, Carpenter (Hill 62).
Referee: Greg MacDonald