Home striker Wayne Gray lofted an early chance inside Rovers' six-yard area high over the bar, but atoned when he converted a 12th-minute penalty after he had been brought down by keeper Steve Phillips, who was fortunate to escape with only a yellow card.
But Rovers equalised on the half hour when striker Rickie Lambert met a cross from Stuart Campbell with a header from the six-yard line for his 13th league goal of the season.
Rovers were desperately close to taking the lead when Sean Rigg, having set Chris Lines clear, just failed to reach his cross at the far post.
Ibehre, on for the injured Gray at half-time, headed against a post and had an effort pushed away by Phillips for a corner, before Boyd restored Orient's lead with his 14th goal of the season after 81 minutes.
Ibehre then scrambled home a third in the final minute to leave Rovers with only one win in 15 matches.