The Swiss netted the two away goals they required but Braga claimed a draw on the night and edged through to the last-16 of the Europa League.
Braga held a spirited Sion to a 2-2 draw at Estadio Municipal to secure a place in the last 16 of the Europa League.
Paulo Fonseca's team prevailed 4-3 on aggregate but were made to worry by their Swiss opponents, who twice took the lead during the first half through Theofanis Gekas.
The veteran Greek striker opened the scoring with an impudent backheel in the 16th minute and scrambled home before the half hour, immediately responding to Josue's penalty for Braga after a Ebenezer Assifuah handball.
Nikola Stojiljkovic turned home three minutes after half-time with what would prove to be the decisive goal but there was drama in stoppage time, with Sion chasing an away goals aggregate victory.
They were agonisingly close as Vincent Rufli rifled a first-time shot against the crossbar from 20 yards and Braga survived.
- Goal