Angry fans clashed with police on the pitch at the Memorial Stadium after Colin Daniel scored the only goal of the game, ensuring Rovers lost their Football League status for the first time since 1920.
Rovers had eased their fears of being relegated along with Torquay United when they beat fellow strugglers Wycombe Wanderers last weekend, a victory that left them two places above the drop zone heading into the final day.
There was a twist in the tale on a dramatic final day, though, as Wycombe won 3-0 at Torquay and Northampton Town beat Oxford United 3-1 to ensure Rovers went down on goal difference.
Darrell Clarke's side were just three goals worse off than Wycombe, who stayed up by the skin of their teeth courtesy of strikes from Sam Wood, Matt McClure and Steven Craig.
Rovers struck the crossbar on three occasions as they pressed for an equaliser that would have been enough to keep them up, but it was not to be and there were ugly scenes as supporters charged onto the pitch after the final whistle.
Chris Wilder mastermined Northampton's great escape by beating the club he walked out on to take over at Sixfields, but Town had to come from behind to seal three precious points.
Ryan Williams put Oxford in front before he was then sent off for kicking Ricky Ravenhill.
Northampton took advantage with goals from John Marquis, Ivan Toney and Mathias Kouo-Doumbe keeping them up.
There were jubilant scenes at Chesterfield as they were crowned champions on the final day after coming from behind to beat Fleetwood Town 2-1.
Matty Blair looked set to spoil the party when he put Fleetwood, who will play York City in the play-offs after finishing fourth, in front.
However, two goals in the space of four second-half minutes from from Sam Hird and Gary Roberts clinched the title for the Derbyshire club.
Scunthorpe United had to settle for second place after they drew 2-2 with York, while Rochdale finished third following a 2-1 defeat against a Newport County side that had to see out the last seven minutes with 10 men after Ryan Jackson was dismissed.
Southend United beat Burton Albion 1-0 at Roots Hall to seal fifth spot ahead of their opponents, who they will now face in the play-offs.
Danny Hollands scored a hat-trick as Portsmouth drew 3-3 with Plymouth Argyle; Accrington Stanley beat AFC Wimbledon 3-2 and Dagenhan & Redbridge were 3-2 winners at Cheltenham Town.
Exeter City signed off for the season with a 2-0 victory at Hartlepool United, while Lancashire rivals Morecambe and Bury played out a goalless draw.
