Wing Dougie Flockhart scored all the Doncaster points as the visitors became the first side to win at Goldington Road this season.
Knights, who fielded an unchanged side, trailed13-3 at the break having played up the infamous slope and into a gale-force wind.
Bedford No 8 Joel Conlon took advantage of some uncharacteristic tackling as he charged past three men to score on eleven minutes.
Fly-half Jake Sharp, who had hit the post with an early penalty, tagged on the extras and also kicked a penalty to make it 10-0.
It took Knights , for whom Flockhart went close following a catch and drive, until the end of the first quarter to breach the Bedford 22.
They didn’t come away empty-handed,however, and the Scot cut the deficit – soon cancelled out by Sharp - with a penalty,
Knights squandered good possession when well placed on a couple of occasions and full-back Steffan Jones was short with a huge penalty at the other end.
Doncaster No 8 Ollie Stedman went agonisingly close after charging for the line from a lineout. Knights had been much more prominent in attack in the second quarter but rode their luck when, with their defence stretched, Bedford failed to capitalise.
Flockhart had the chance to cut into Bedford’s lead with a penalty he would normally have kicked in his slippers on the stroke of half-time, only to come up short.
But it was a confident Doncaster side which took to the field after the break, even more ao when Flockhart kicked a second penalty within a couple of minutes.
Flockhart was wide with a subsequent penalty on the halfway prior to full-back Paul Jarvis pulling off a crucial tackle on Bedford centre Tom Griffiths.
Knights went close from a catch and drive prior to Flockhart’s third penalty on the hour. The Championship’s top points scorer also hit the target seven minutes later to leave just one point separating the two sides.
Bedford hit back and but for the combined efforts of Latu Makaafi and Jarvis, Wales Sevens international Jones would have been in at the corner. Flockhart edged Knights into the lead (15-13) for the first time with a long-range penalty on 74 minutes. And he gave them breathing space with a sixth penalty in the last minute of normal time.
Doncaster Knights: Jarvis; Flockhart, Clark. Hurrell, Lewis; Cusack, Heaney; List, Hunter, Quigley,Challoner, Phelan, Shaw, Hills, Stedman. Rep:Bergmanas, Veikoso, John, Makaafi, Bulumakau, Edgerley, Young.
* “It makes pleasant reading to be second in the table at the midway point of the league campaign,” said director of rugby Clive Griffiths
“We’ve got to be pleased with the result because they were unbeaten at home and are the only side apart from ourselves to have beaten Bristol this season.
“Goldington Road is a tough place to come what with the slope and various contours and the conditions made it even tougher.
“We won the toss and we elected to play up the slope and into the strong wind as I’m sure they would have done.
“The plan was that we’d come in at half-time sufficiently close to them so we wouldn’t have to start forcing passes in the second half to get back into the game which would have been very risky in that wind.
“They got off to a good start and scored a converted try, which I wasn’t too happy about defensively, but I was happy to come in just 13-3 down.
“We won the second half 15-0 and we also went close to a try on a couple of occasions.
“They broke us twice but we scrambled back well and I thought our outside defensive line was really good.
“The forwards did well at set-pieces again and the boys who came off the bench again made a tactical impact.”
Prop Jack Bergmanas faces a spell on the sidelines after suffering a knee injury.