Jesualdo Ferreira's struggle to keep Braga in their usual lofty position in the Primeira Liga saw him depart the Estadio AXA in February, with Jorge Paixao taking charge for the rest of the season.
Paixao led the club to ninth in the Portuguese top flight, their lowest league placing in over a decade.
Conceicao's Academica finished a place above Braga in the table, courtesy of a superior head-to-head record.
In the previous campaign, Conceicao kept Academica in the top flight having been appointed towards the end of the season.
The former Portugal winger made 56 appearances for his country, scoring 12 goals, and won three Primeira Liga titles as a player with Porto.
Braga were eliminated from both cup competitions at the semi-final stage, but failed to reach the UEFA Europa League group phase after a play-off defeat to Romanian outfit Pandurii Targu Jiu.
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