The Brazil midfielder crashed in a second-half volley to keep the Hammers on top of Group A and to the brink of qualifying for the knockout stages.
It was also a measure of revenge for West Ham, who had accused the Greek team of celebrating their 2-1 win in the reverse fixture two weeks ago as if they had won the Europa League itself.
Olympiacos fans created a hostile atmosphere that night in Athens, unfurling a huge banner across one stand reading ‘Tonight you dine in hell’.
The London Stadium, by contrast, could never be referred to as a cauldron of noise, and besides, ‘Tonight you dine in Westfield’ does not have the same ring to it.
Nevertheless, the place was crackling at kick-off with the Hammers, last season’s Europa Conference League winners, in need of a victory to keep their continental destiny in their own hands.
But a workmanlike but limited Olympiacos proved a tough nut to crack in the opening 45 minutes.
Said Benrahma dragged an early shot wide and then saw a better one saved by visiting goalkeeper Alexandros Paschalakis.
From the corner James Ward-Prowse’s cross was headed straight at Paschalakis by Nayef Aguerd.
Jarrod Bowen, on the day he earned another call up to the England squad, nodded Vladimir Coufal’s cross wide before Paschalakis was called into action again by Benrahma’s low drive.
Two more Aguerd headers were off target before Olympiacos had their first shot in anger, shortly before half-time, with on-loan Wolves forward Daniel Podence volleying Francisco Ortega’s cross wide.
Ward-Prowse should have given his side the lead on the hour when he met a cutback from Bowen, but the midfielder’s shot was straight at Paschalakis.
But Paqueta, the best player on the pitch, finally broke the deadlock after Bowen’s square pass found Ward-Prowse.
The former Southampton midfielder chipped it forward into the area for Paqueta to fire home on the volley from.
The goal was initially ruled out by an assistant referee’s flag, but a VAR check showed the Brazilian was onside and referee Matej Jug, who had infuriated West Ham with some strange decisions all evening, got the biggest cheer of the night when he signalled a goal.
It was a fourth assist in four European outings for Ward-Prowse, who was overlooked by England again earlier in the day, more than a year after his last call-up.
Paqueta pointedly went to the 3,000 travelling fans to celebrate, probably because the West Ham players were targeted by laser pens from Greek supporters in Athens.
West Ham survived a late scare when Mady Camara rattled a post but they held on to complete their European revenge mission.