Alderweireld had to be taken off on a stretcher during Saturday's 1-1 draw with West Brom and although the injury isn't as serious as had been first feared, he will not be involved in Germany on Tuesday.
Dier replaced him at centre-half against Albion and could be handed a starting spot in defence at the BayArena in the Champions League meeting in the Belgian's absence.
Pochettino has mainly used Dier as a defensive midfielder after signing the 22-year-old in the summer of 2014, his first transfer window at White Hart Lane, but the England international played at centre-half for previous club Sporting Lisbon and the Spurs boss is confident he can impress at the heart of defence.
"The important thing is we trust in him," said Pochettino. "It's not important the position he will play - midfield, centre-back or full-back - we believe and trust in him.
"We trust him as a person and his skills. For me, Eric is a player who can develop his game in different positions."
Striker Harry Kane remains absent with an ankle injury but he is closing in on a first-team return, while defender Kyle Walker has been rested and will not be involved on Tuesday night.