Greece midfielder Stelios Giannakopoulos opened the scoring for the home side after 25 minutes, heading home from close range.
However, striker Kevin Phillips levelled on 69 minutes with a right-foot shot to deny the hosts the chance of moving into the final Champions League spot.
The result left Bolton in fifth on 53 points from 34 matches, a point behind Everton who have two games in hand.
Southampton edged out of the relegation zone on goal difference. They are level on 28 points with third bottom West Bromwich Albion, who have two games in hand.
In Tuesday's other match, Middlesbrough drew 1-1 with Fulham who nudged up one place to 15th on 35 points.