Southampton had the better of the first half and saw Nathaniel Clyne miss a great chance before Rickie Lambert's free-kick was superbly turned onto the post by Hugo Lloris.
But, with four minutes to go, Saints old boy Bale cut in from the right and fired a powerful shot beyond Artur Boruc to keep Spurs on course for the UEFA Champions League.
Pochettino, whose side have beaten Manchester City, Liverpool and Chelsea since he took charge, was disappointed not to claim another notable scalp.
"Yes, we played a very good game today and we deserved to leave this game with a result," Pochettino told Sky Sports.
"What's really important is that we competed and during long spells of the game we actually played better than Tottenham.
"But it's a shame not to get anything from out of this game."