Slavia Prague were awarded a penalty when Nigeria international, Peter Olayinka, was tripped by Stefan de Vrij, which was converted by captain Soucek but still went down 3-1 to Inter Milan.
Inter are in the second qualification spot in Group F with one game left.
The Italians are level on points with Borussia Dortmund, but have a better head-to-head record.
It means Inter, who host group leaders Barcelona on 10 December, will qualify if they at least match Dortmund’s result at home to Slavia.
Lukaku, who now has 198 club goals and 52 for Belgium, also had two goals disallowed in the Czech Republic.
Inter’s club record signing cut back for Martinez to open the scoring before his team-mate returned the favour, only for the video assistant referee to rule there had been a foul at the other end moments earlier.
Inter hit the crossbar twice in four minutes after the break, through Lukaku’s 65th-minute header and a 25-yard volley by Marcelo Brozovic.
But the Italian outfit restored their lead as Martinez let Valentino Lazaro’s through-ball run and defender Michal Frydrych slipped, allowing Lukaku to run through on goal before taking the ball round Ondrej Kolar and firing into an empty net.
Soucek almost equalised moments later as he sidefooted wide from close range following a free-kick but Inter sealed victory as Lukaku delivered a superb cross with the outside of his left foot for Martinez to volley home.
Lukaku thought he had scored again with a low shot in stoppage time but the goal was ruled out for offside.