Lorient appeared to be on course to halt a run of three straight Ligue 1 defeats by claiming a valuable away point.
However, Henrique struck in the 89th minute to ensure Sylvain Ripoll's men still languish in the relegation zone.
Rennes enjoyed the majority of possession in the opening stages and Kamil Grosicki threatened to open the scoring when he flashed over the crossbar from the edge of the box after cutting in from the right.
At the other end Lorient almost stole ahead in fortuitous circumstances when Walid Mesloub's deflected shot left Rennes goalkeeper Benoit Costil stranded, but the ball went wide of the goal.
The second half proved just as tense, although Lorient's Raphael Guerreiro forced Costil into a smart save low to his left with a close-range effort.
Just when it looked like the game would end in stalemate, Rennes broke the deadlock with a devastating counter-attack.
Paul-Georges Ntep managed to get to the byline and his cross from the left was deflected by Vincent Pajot into the path of Henrique, who prodded home from inside the six-yard box to secure the points for Philippe Montanier's side.
