The Belgian defender was among the heroes for Spurs as they delivered a European miracle against Ajax.
Mauricio Pochettino’s side had headed to Amsterdam on Wednesday trailing a semi-final tie 1-0 on aggregate, and fell a further two goals behind before half-time.
Lucas Moura was, however, to inspire a remarkable turnaround with a second-half hat-trick, with Spurs edging through on away goals.
Vertonghen was able to play a full part in proceedings against his former club.
He was among those to race after Lucas once the Brazilian netted the most dramatic of 96th-minute winners.
The 32-year-old was, however, absent from the post-match celebrations.
The Spurs players, and manager Mauricio Pochettino, returned to the field after the game to acknowledge their supporters and revel in the most memorable of continental successes.
Little attention was paid to Vertonghen’s no-show at the time.
He was, though, caught on camera by HLN departing the Johan Cruyff Arena via the back door as the cause of his absence became clear.
It is mandatory for players to pass through the mixed zone after Champions League games, but Vertonghen was kept out of sight.
That is because he was hobbling around on crutches and sporting a protective boot on his right foot.
The extent of the injury is not yet known, but the outlook does not look good.
Spurs are due to face Liverpool in a European showpiece at Wanda Metropolitano on June 1.
That gives Vertonghen a little over three weeks to recover from his ailment.
Tottenham are said to be waiting on the results of a scan before making a full assessment.
They had already nursed Vertonghen through one injury in order to get him onto the field against Ajax.
A clash of heads in the first leg of a meeting with the Eredivisie giants had sparked concussion fears and left the Belgian with a cut on his nose.
He had worn a face mask in the return date, but now appears to have suffered a fresh setback in his bid to help Tottenham to a first European Cup triumph.