The home side, narrow bookmakers' favourites to win Group A despite their lowly 40th world ranking, fell behind to an Ivan Perisic goal in the sixth minute.
Guillaume Gillet equalised on the stroke of halftime but despite Belgium's neat footwork which created chances, they could not find a winner.
"If there was one team that merited a victory it was Belgium. We have lost two points at home. It annoys me a bit," said Belgium coach Marc Wilmots. "Still, if you can dominate Croatia for 80 minutes, it is a good performance."
"If I look at international football, getting six or seven chances in a match is a lot, but you need the killer touch," he continued.
Perisic drove in an easy opener when Vincent Kompany failed to fully clear Darijo Srna's cross.
Gillet, the sole home starter still playing for a Belgian club, thundered in an equaliser from a half-cleared corner in the final seconds of the first half.
Belgium talked before the match of shutting down Croatia midfielder Luka Modric, but it was wingers Srna and Perisic and imposing striker Mario Mandzukic who threatened most, while their defence was disciplined throughout.
Belgium, with six of their starting 11 playing in England's Premier League, threaded the ball neatly across a midfield featuring Eden Hazard, Axel Witsel and Moussa Dembele, all big money signings for the new season.
Belgium's wealth of individual talent has prompted talk of a golden generation emerging after a decade-long barren spell with continued failure to qualify for a big tournament since the 2002 World Cup.
Brussels' King Baudouin stadium was for the first time in years a 40,000 seat sell-out for the second straight match, many fans heeding the Red Devils call for them to dress in the national colour. Gillet's equaliser ignited the crowd, which roared the team on for a winner.
Croatia coach Igor Stimac described the match as a point gained.
"If you lose at home you make it difficult for yourself. You have to win home games," he told reporters. "We should be happy winning at home and getting a point from the biggest opponent in our group."
Stimac said Group A appeared to be narrowing down to a contest between Belgium, Croatia and Serbia, all with four points after two matches.
Serbia's 6-1 demolition of Wales put them top on goal difference, with Belgium in second and Croatia third.
