A superb first senior international goal from Lukas Provod put an impressive Czech Republic side in front five minutes into the second half at Sinobo Stadium.
Belgium came from behind to beat Wales in its first UEFA Group E game in midweek and it rallied once again to secure a point courtesy of Lukaku’s seventh goal in his past six games for the Red Devils.
Both sides struck the woodwork in an entertaining contest, but had to settle for a draw that leaves them with four points apiece from two matches early in their bids to qualify for the tournament in Qatar next year.
Lukaku fired over and Dries Mertens had an early shot palmed wide by Tomas Vaclik in a promising start for the world's No.1 international side.
The Czech Republic sensed Belgium was there for the taking as the rain continued to lash down and Michael Krmencik cut inside Jason Denayer before striking the outside of the near post with a left-footed strike 16 minutes in.
There was no let-up in a pulsating first half and Vaclik produced a magnificent one-handed save to keep out Leander Dendoncker's rasping drive, before Kevin De Bruyne failed to generate any power on Lukaku's cross with a close-range header.
It was the home side that got the breakthrough early in the second half with a brilliant finish from winger Provod, who found the far corner of the net with a venomous right-foot finish from 20 yards out after being picked out by Jakub Jankto.
Belgium was only behind for 10 minutes, though, as De Bruyne threaded a ball through to Lukaku and the striker turned Ondrej Celustka inside-out before finding the back of the net with a finish Vaclik might have been disappointed not to keep out.
De Bruyne almost put Roberto Martinez's men in front but saw his right-foot strike come back off the outside of the post and Jan Boril hit the crossbar with a measured late drive at the other end.
Tomas Soucek, who was captain of his country for the first time, went agonisingly close to snatching a dramatic win right at the end when Toby Alderweireld nodded his looping header off the line, so it ended honours even.