Arsenio Cabungula scored in the 23rd and 90th minutes for the Angolan club as they secured a 3-2 aggregate victory.
Goalkeeper Brandon Petersen had to be alert in the fifth minute to save one-on-one after a defensive error as the hosts made a nervy start to the game, before Cabungula opened the scoring.
Toriq Losper made the visiting keeper work in the 30th minute with a shot from range, and then tested him again three minutes later but was unable to score.
Ajax had a penalty appeal waved away just before half-time when Bantu Mzwakali went down in the area and Franklin Cale had a go from distance in the 56th minute.
Then the game went through a bit of a lull as Ajax became happy to hold onto possession, as they were still leading on away-goals despite the 2-2 aggregate score at the time.
Mzwakali had a chance to equalise in the 84th minute from substitute Riyaad Norodien’s cross but his header went over the bar, and Losper had a chance two minutes from time but also shot wide.
Then came the killer blow right at the death as Cabungula popped up again to make it 2-0 on the night and 3-2 to Sagrada on aggregate.
Ajax: Petersen, Mabaso, Lartey, Lebusa, Langwe, Graham, Cale (Norodien 79'), Losper, Mzwakali, Gamildien (Coetzee 53'), Nxumalo (Morris 69')