Freiburg thumped Olympiacos 5-0 in the section's other match and had looked to be moving into first ahead of their trip to the English capital on December 14.
However, Tomas Soucek's late goal moved the Hammers onto 12 points in the section, level with Freiburg, and the pair will go head-to-head for the automatic spot in the round of 16 next month.
Second spot in the section brings a position in the knockout round playoffs, demonstrating the importance of the contest between the top two at the London Stadium, and West Ham have an advantage due to their superior head-to-head record against the German side, winning the reverse fixture 2-1 in October.
The hosts had the first opportunity of the match in the seventh minute, but West Ham goalkeeper Lukasz Fabianski made an excellent save to deny Uros Milovanovic, who had met a cross from Milos Cvetkovic.
The hosts came close again in the 21st minute through Nikola Kuveljic, but his effort from distance was over the crossbar, with West Ham struggling to get going in the Group A fixture.
Fabianski was forced to make another smart save in the 31st minute, with the experienced goalkeeper keeping out a strike from Aleksandar Cirkovic, before Said Benrahma had an effort kept out by Veljko Ilic, with the strike proving to be West Ham's first attempt on target.
The Hammers had another opportunity in the closing stages of the first period, but Soucek's header from a James Ward-Prowse free kick was always drifting wide of the post, and a largely uneventful first period ended with the two teams level at 0-0.
Fabianski made an excellent save to keep out a strike from Milovanovic just past the hour, but West Ham were still struggling in the final third, and both Danny Ings and Maxwel Cornet were introduced in the 67th minute.
Lucas Paqueta had a long-range strike deflected over the home side's crossbar in the 72nd minute, but the pressure was building, and West Ham managed to make the breakthrough in the 89th minute through Soucek, who volleyed a wonderful cross from Cornet into the back of the net.
Soucek came close to another late on from a Ward-Prowse free kick, but one goal ultimately proved to be enough for David Moyes's side to claim all three points.
West Ham will return to Premier League action at home to Crystal Palace on Sunday, while Backa Topola will resume their Serbian Super Liga campaign against Radnicki Nis on the same afternoon.