Admir Mehmedi put Switzerland ahead five minutes into the Group B game by converting a penalty he was forced to retake after Innocent Emeghara was brought down inside the area.
Pierre Aubameyang equalized when he collected Alexander Ndoumbou's floated cross alone inside the area in the 45th and flicked a shot under goalkeeper Diego Benaglio.
Switzerland finished with 10 men after Oliver Buff was shown his second yellow card in the 78th for theatrically going down under little pressure as he burst into the African nation's area.
"I saw some great things but our game lacked consistency," Switzerland coach Pierluigi Tami said after his team's first appearance in the competition for 84 years. "But I was hoping to go into the break leading 1-0 so I could correct certain things."
Gabon can certainly come away from its opening game buoyed by its effort after only having 15 players available at St. James Park after last-minute addition Samson Mbingui was approved to join. Gabon's squad has been set back by injuries and clubs refusing to release overage players.
"Sure it's difficult to play with this configuration and with so many replacements," said Gabon coach Claude Mbourounot. "We just play the cards we're dealt and hope we can make it."
All four teams in Group B have one point after Mexico and South Korea drew 0-0 earlier on Thursday. Switzerland plays South Korea next on Sunday, when Gabon faces Mexico.