Boss Mark McGhee's side conceded an early own goal and then a penalty which led to a red card for young defender Daniel Harding.
Plymouth went ahead in chaotic fashion in the 10th minute with a free-kick from long range by Paul Wotton which forced Michel Kuipers into a diving save. Danny Culip headed against his own post in the scramble that followed and the linesman flagged to indicate the ball had crossed the line.
Brighton's chances of retrieving a result effectively evaporated in a six minute period before half-time. Harding followed a booking for a rash tackle on Lee Hodges with a push inside the penalty area on Marino Keith.
He was sent off by referee Andy Hall for a second bookable offence before Wotton drilled in the resulting spot-kick. There was no way back for Brighton after that, but they managed to avoid further embarrassment in a spirited second half.
The one bright spot for McGhee was an encouraging home debut of 21-year-old Alexis Nicolas, a central midfielder on loan for 32 months from Chelsea.
Argyle, meanwhile, are sitting pretty with four points and no goals conceded in their opening two games.
They could have won even more convincingly but for some inaccurate finishing in the first half by Keith, who was preferred up front to Mick Evans.