Jay Rodriguez broke the deadlock inside 20 minutes and Adam Lallana quickly added a second as Saints made a great start at White Hart Lane.
However, Christian Eriksen scored either side of half-time to bring Spurs level and Gylfi Sigurdsson's injury-time strike left Southampton with nothing to show for their efforts.
Pochettino still believes the future is bright for Southampton, however, after performing well against a Tottenham side with a much stronger squad.
"I think Tottenham are a team that are actually equipped to be a candidate to win the league," Pochettino told Sky Sports.
"For Southampton, we are a young team with young players, so it is a long-term project for Southampton.
"Despite that, I thought it was an even-sided game, but we are disappointed with today's result."