The Belgian striker now has four goals in as many games, and his predatory instincts 21 minutes from time masked the flaws in Thomas Tuchel's side's performance.
Tuchel encouraged his players not to rest on their laurels following their unexpected European title triumph last season.
However, the glory of their triumph against Manchester City in Porto was impossible to ignore, as the German, Edouard Mendy, and Jorginho were presented with UEFA coach, goalkeeper, and player of the year trophies on the pitch before kick-off.
Chelsea has the squad depth to compete on all fronts this season, and Tuchel made five changes from the team that defeated Aston Villa 3-0 in the Premier League on Saturday.
Chelsea's forward style lacked energy throughout, despite the return of captain Cesar Azpilicueta, Andreas Christensen, Reece James, Jorginho, and Mason Mount to the starting lineup.
The first half passed without the home team recording a single shot on goal.
Centre-back With a ferocious surge forward five minutes after the half, Antonio Rudiger appeared to take matters into his own hands, but his finish let him down as he blasted wide.
Lukaku scored his first Stamford Bridge goal for Chelsea against Villa at the weekend, displaying his blend of quickness, power, and accuracy in front of goal.
The 28-year-old had been kept quiet for over 70 minutes by Zenit, but all he needed was one enticing cross from Azpilicueta to get his new team off to a winning start in the Champions League by landing a header beyond Stanislav Kritsyuk.
In quest of an equaliser, Zenit coach Sergei Semak brought on the imposing presence of Artem Dzyuba, and it almost paid off.
But, with 10 minutes to go, even the six-foot-six-inch (1.97-metre) Russian international couldn't get a clean enough contact on Sardar Azmoun's cross, and the ball dribbled wide.
With the arrival of Thiago Silva, Tuchel put an end to the attack, as Chelsea kept their fourth clean sheet in six games this season.