JAKARTA (AFP) - The Southeast Asian Games was to close Tuesday with sporting success for Indonesia overshadowed by a stampede at the headline football final which left at least two people dead and a young boy in a coma. With final preparations underway for Tuesday night's closing ceremony in Palembang, the event was tarnished by the tragedy in co-host city Jakarta where the hosts played bitter rivals Malaysia for football gold late Monday. Two victims died in a crush before the match when stadium gates were opened and the crowd surged to get in, Jakarta police told AFP, adding that a boy taken to hospital had slipped into a coma. Games organisers Inasoc had warned of the potential for flashpoints ahead of the highly-anticipated final -- which defending champions Malaysia won 4-3 on penalties after the teams were deadlocked at 1-1 after extra time. Monday night's events took the sheen off glittering Games for the hosts, who had collected 182 golds in a bulging total medal haul of 475 with only paragliding finals to be contested Tuesday afternoon. It meant Indonesia topped the Games medals charts for the first time since 1997 -- when they last hosted the competition -- and left 2009 winners Thailand trailing on 107 golds, followed by Vietnam with 96. The gold most craved by the home fans was in the headline under-23 football, but instead they endured heartbreak as Malaysia's captain Baddrol Bakhtiar scored the winning penalty, following two missed spot-kicks by Indonesia. The visitors showed their mettle in coming back from a goal down in front of the hostile home crowd, earning praise in their domestic media Tuesday, with the Malaysia Star newspaper hailing their win as "the mother of all golds". Chasing their first Games football gold for two decades, Indonesia looked set to secure victory after centre-back Gunawan Dwi Cahyo headed in a corner after five minutes. But Malaysia fought back, silencing the crowd with an equaliser by Omar Muhammad Asraruddin around the half-hour mark, and then defending resolutely to take the game to penalties. Indonesian coach Rahmad Darmawan told the Jakarta Post that his players were reluctant to take the spot kicks. "Only three players said they were ready for the shootout, while others needed to be encouraged," he was quoted as saying. "I express my apology to Indonesian fans for my failure to meet their highest expectations." The only nation of the 11 taking part in the biennial Games without a gold medal was tiny Brunei. Indonesia has faced widespread criticism for a raft of problems that dogged the run-up to the Games, including building delays and shortages of accommodation and transport. The troubles prompted Myanmar's chef-de-mission to vow his nation will do a better job when they host the next Games in 2013.