In what turned out to be the last kick of the game against Shakhtar in the Champions League, Alderweireld had the chance to equalise from the spot in the seventh minute of stoppage-time.
However, the ex-Tottenham defender dragged his effort well wide as he appeared to mishit the ball.
As the final whistle blew, he was consoled by his teammates as he looked visibly gutted to have missed the chance to grab a point.
Antwerp manager Mark van Bommel also put an arm around the 34-year-old, who moved to the club in 2022.
The Belgian side had gone two goals up against Shakhtar on Wednesday night in one of the earlier kick-offs, through Arbnor Muja and Michel-Ange Balikwisha.
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But the Ukrainian outfit came back after half-time when Danylo Sikan and Yaroslav Rakitskyi brought it back to 2-2, before Sikan netted his second to make it 3-2.
Belgium international Alderweireld's missed penalty meant that Antwerp relinquished all three points, leaving them with zero points after two games in Group H.
This was a crucial fixture, as well, considering that Barcelona and Porto are the two heavy favourites to qualify from the group.
Nevertheless, reaching the Champions League is a fairytale story for Antwerp, who have made it to the competition for the first time in their history.
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They did so in dramatic style by winning the Jupiler Pro League in the final minute last season with Alderweireld scoring the goal to secure the title.
The defender spent six seasons at Tottenham from 2015 to 2021 and is well-remembered by their fans, forging a strong partnership with countryman Jan Vertonghen in north London.
In total, he made 236 appearances for Spurs before leaving for Al Duhail in 2021 in Qatar, joining Antwerp a year later.