Both teams were evenly matched and it was the 15-time champions who had the lion's share of possession over Gabon - who featured two English Premier League players in Watford midfielder Ndong Didier Ibrahim and Southampton midfielder Mario Lemina - but neither could find a breakthrough as the match went to penalties after a goalless 90 minutes.
Milovan Rajevac's side will fancy their chances of winning a 16th title on Sunday, while AFC Asian Cup 2019 hosts UAE will meet Gabon in the third-place play-off.
In the earlier match, Slovakia secured a 2-1 victory over the United Arab Emirates.
Slovakia, who were missing talisman Marek Hamsik in their lineup, took the lead three minutes before the break through Albert Rusnak.
Michal Duris added their second in stoppage time to give Jan Kozak's side a comfortable 2-0 lead at half-time.
Slovakia, who won the tournament in 2004, maintained their two-goal advantage for the most part of the second half before Alberto Zaccheroni's side pulled one back.
Ahmed Khalil's 73rd minute effort following a Rayan Al Jaberi assist put the score at 2-1 but Slovakia held on to advance to the final.