David Moyes' side always knew it was going to be a difficult night against a Belgian side that had pushed Liverpool so close in the Champions League last month, and so it proved.
Moyes, rumoured to be on the verge of signing a new long-term deal with the Toffees, welcomed Leon Osman back into his starting line-up after a three-week injury absence, the midfielder replacing the ineligible Marouane Fellaini.
Everton started brightly and Victor Anichebe fired an early ten-yard shot wide before last season's impressive Belgian League winners, took a tenth-minute lead.
Joleon Lescott, who endured a poor evening, was at fault as Wilfried Dalmat crossed for Dieumerci Mbokani to guide a close-range shot home.
The goal rocked Everton and they almost slipped two goals behind midway through the first half when Igor de Camargo deflected Milan Jovanovic's shot wide
Against the run of play, Everton grabbed an equaliser thanks to Yakubu's goalscoring instincts. The Nigeria international found the net from ten yards out after good play by Lescott, Mikel Arteta and Osman.
Back came Standard though, and after Jovanovic had wasted a good opportunity to regain their lead, Marcos Camozzato's low cross was turned into his own net by the unfortunate Joseph Yobo to make it 2-1 to the visitors.
Everton were level again though in the 38th minute when Ecuadorian midfielder Segundo Castillo's spectacular long-range effort flew past Rorys Aspinoza.
The second half could not live up the first 45 minutes and, although Everton did most of the pressing, Standard continued to look lively on the break.
Anichebe had to be stretchered off the pitch and was replaced by James Vaughan who went closest to grabbing an Everton winner when he guided a late header wide.
In stoppage time, Standard thought they should have had a penalty when Lescott appeared to trip Dalmat, but the referee was unimpressed and waved play on to the home fans' relief.