Vladimir Darida had fired Freiburg ahead after 11 minutes but Seba levelled soon after the interval, and the teams cancelled each other out thereafter.
Portuguese outfit Estoril, who are playing in Europe for the first time and are based further west on the map than any other team in the competition, came into the match without a point from their opening two games, after losing to Sevilla and Slovan Liberec, while Freiburg had lost to the Spaniards but drawn with Liberec.
They have significant catching up to do over the remaining three rounds of games, and Estoril will be looking to make home advantage count when the teams that contested Thursday's game do battle again in Portugal in two weeks' time.
Freiburg boss Christian Streich watched his team start brightly, with Vegar Eggen Hedenstad and Admir Mehmedi both causing flutters of concern for Estoril with early shots at Vagner's goal.
The Brazilian goalkeeper was initially defiant but Darida found a way past him with a large slice of luck.
Receiving the ball in a position to the left of goal, and needing a Hollywood finish to beat Vagner, Darida put his head down and cracked a fierce shot that took a hefty deflection off Yohan Tavares and squeezed inside the near post.
Vagner had no hope, having followed the initial flight of the ball and moved in the opposite direction.
The goalkeeper parried a strike from Julian Schuster as Freiburg looked to strengthen their position, but Estoril restricted the damage to one goal at the break.
Their resilience was rewarded in the 53rd minute when Vagner's compatriot Seba equalised.
The striker held his run perfectly before tearing beyond the home defence to prod Luis Leal's pass through the middle underneath goalkeeper Oliver Baumann.
Darida tried his luck but missed the target as Freiburg looked to reclaim the lead, while Estoril began to think of the win, with former Hannover man Carlitos seeing a 20-yard shot saved by Baumann.
Francis Coquelin, the on-loan Arsenal midfielder in Freiburg's ranks, had the final shot of the game that demanded a save, with Vagner proving up to the task.