Agogo was first to a knock down from team-mate Lee Thorpe as rifled his 67th minute shot past Lincoln keeper Alan Marriott into the bottom corner.
But as they celebrated Agogo appeared to make an obscene gesture towards his own bench.
Referee Fred Graham produced a red card for the striker and then booked Thorpe for protesting at the decision.
The drama was in stark contrast to the rest of the dire game between two teams who still have hopes of at least a play-off spot in May.
Lincoln began brightly and were close to taking the lead in the eighth minute.
Francis Green found himself unmarked six yards from goal and hit in the low shot only for Rovers keeper Ryan Clarke to make an excellent save at point blank range.
Lincoln completely dominated the first half with Rovers unable to manage either a shot or a corner.
But Clarke rarely found himself under pressure with Lincoln unable to get their shots on target.
The home team almost broke the deadlock in the 40th minute when Ciaran Toner floated a free-kick into the Rovers box. Clarke was caught of his line and beaten by a header from Gareth McAuley but Rovers were saved by the crossbar.
Rovers came forward more after the break but Lincoln still looked more likely to score.
Clarke made a spectacular save in the 59th minute to keep out a header from Craig Westcarr and Jamie McCombe's follow up shot went over the bar.
Lincoln went in front after Rovers' James Hunt was yellow carded for a foul on Gary Taylor-Fletcher.
Toner sent a free-kick into the box but Robbie Ryan made a hash of his clearance. The ball came back to Matthew Bloomer who set up Green for a simple goal.
After Agogo's equaliser, Rovers almost smashed a late winner when substitute Craig Disley got clear of the Lincoln defence only to see his shot saved by Marriott.