Vertonghen was in the stands watching the game on Saturday after Toby Alderweireld and Davinson Sanchez started at centre-back.
Speaking to Sky Sports (h/t Rob Guest of Football.London) about Vertonghen's absence and his starters, Pochettino said the players who did not feature against Villa need to "work hard" to be selected in the future after the 3-1 home victory.
"I want to play the players who deserve to play, who I think to deserve to play and who are playing well. My decision today was to play Toby. If the players didn't play today, they need to work hard to get their opportunity.
"With all the players fit you struggle to find a starting 11. We have more than 25 players and everyone needs to understand we have plenty of good players in every position. We can only play with 11.
"It's always the judgement of the manager and the coaching staff."
Villa were Spurs' equals for large parts of the game, and the promoted team claimed a shock lead through John McGinn after just nine minutes. The Scot was composed in the box as he was challenged by Danny Rose, and he slotted away with a clinical finish.
However, Spurs were the better side in the second half, and Dean Smith's team fatigued in the final 10 minutes. Tanguy Ndombele grabbed the equaliser on his debut after 73 minutes, and Harry Kane scored twice in the final four minutes.
Pochettino blamed himself for his team's slow start, saying the opener was a "crazy goal" and added his players were "confused" in the first half—per Sky Sports:
Vertonghen featured regularly in pre-season, so his absence was noticed when the teams were announced. The defender has just one year left on his deal at Spurs, and he recently admitted he does not know if the club will offer him a new contract. The Belgium international said he is currently "happy" at the club and believes he has Pochettino's "support."
The European transfer windows continue to be open through August, but there is no suggestion Vertonghen will be sold, despite entering the final year of his contract. The player remains an elite defender and will be expected to fight his way back into the starting XI.