Doncaster were hustled out of their stride and missed out on a chance to go top of the table as Lincoln snatched an unexpected victory with a battling display.
Rovers had won nine in a row at home, but were outfought and struggled to match City's commitment and work-rate.
Lincoln's route-one approach was not pretty to watch but it proved effective with Doncaster never able to settle into their rhythm and play their normal passing game.
To add to the home side's misery they put the visitors on the path to victory with an own-goal in the 11th minute.
John Doolan gave the ball away in midfield and Francis Green's cross was turned into his own net by unfortunate defender Tim Ryan.
Leo Fortune-West had a shot on the turn deflected wide and Michael McIndoe had a close-range effort tipped over the bar by Alan Marriott as Rovers tried to hit back.
Lincoln were seldom seen as an attacking force after they had taken the lead but they rocked the home side again when they snatched another goal after the interval.
It came in the 58th minute when Rovers failed to clear their lines following a corner.
Fortune-West headed the ball into the air and Gary Fletcher scored in spectacular style with an overhead kick, with home keeper Andy Warrington protesting he had been impeded.
Adriano Rigoglioso twice went close with thundering free-kicks after coming on as a substitute, but Marriott tipped his first effort over the bar at full stretch and the second was deflected narrowly wide.
Doncaster still had chances in the closing stages but Fortune-West missed the ball completely with the goal at his mercy in the 81st minute before firing straight at Marriott from close range two minutes later.
Green had a shot cleared off the line at the other end before Rovers' misery was complete when Ricky Ravenhill rattled the post only to see the ball bounce to safety four minutes from time.