After coming from behind the Saints looked set to seal the win at the DW Stadium after Morgan Schneiderlin's 85th minute goal, but Shaun Maloney found the net in the last minute to rescue a point for the Latics.
"There are two different feelings," Pochettino told the club's official website. "First because we played well, and secondly, because we could and should have won the game, so we are disappointed with the result.
"I am happy with the performance of the team, and although I am disappointed with the result, we played well today, so I am happy with that."
The Saints are currently 16th in the Premier League and are just three points clear of the relegation zone.