Toney's brilliant backheel opened the scoring midway through the first half before a typically assured finish from the penalty spot ended a three-game winless run for the Bees.
Brighton are still searching for their first win under new boss Roberto de Zerbi and despite enjoying the majority of possession, they posed little threat at the Brentford Community Stadium.
Toney was called into Gareth Southgate's squad last month, but did not get a minute on the pitch in games against Italy and Germany.
But he moved level with Harry Kane as the top English goalscorer in the Premier League this season with eight on his 100th Brentford appearance.
The 26-year-old improvised to flick home Frank Onyeka's cross on 27 minutes.
Brentford boss Thomas Frank rates Toney as the best penalty taker in the world and he was again faultless from the spot after Joel Veltman's mistimed lunge inside the box was punished.
Victory takes Brentford up to eighth, just one point behind Brighton who remain seventh.