The Belgium striker, on as a second-half substitute, lashed in Andros Townsend's cross in the fifth minute of added time to return Palace to winning ways following successive defeats which had led to growing supporter unrest.
Brighton dominated proceedings at the Amex Stadium and levelled through Joel Veltman after the Eagles led at half-time courtesy of a superb, back-heeled finish from French forward Jean-Philippe Mateta.
Palace showed little ambition for much of the match and once again struggled to create in the absence of injured talisman Wilfried Zaha, with the two superb goals their only attempts on target.
Yet Hodgson - who picked Mateta over Benteke - will be more than satisfied with a result which moves his side 10 points above the relegation zone.
"It should make a big difference (to Benteke)," Hodgson told Sky Sports after the game. “You have a squad of players and you can only pick 11 and players that are left out always feel they shouldn't have been left out.
"But when you get the chance to show what you're about, you do what Christian did and take that chance. He thinks I made a mistake by not picking him tonight and he told me that with his performance and goal.
"I am really pleased with the guts and determination and the fight, and I am really pleased with the shape of the team. We kept going and came away with the ultimate points total from the game.
"I am happy with 32 points, but I will be even happier when we have 38 on the board."
Additional reporting by PA.