Jose Mourinho's men, who had been dominant, looked set to be eliminated from European football for the season when Lokomotiv took a 71st-minute lead, but two of the home team's players were dismissed in quick succession and Spurs netted twice in the latter stages to scrape through to the next round.
Spurs had no issue controlling proceedings as they enjoyed 72 per cent of the first-half possession, but they lacked a clinical edge in the final third, with Steven Bergwijn going closest when striking the crossbar early on.
Lokomotiv seemed to have made the most of Spurs' struggles when Georgi Minchev headed them into the lead, but Dinis Almeida was sent off for denying a certain goal – with Harry Kane subsequently netting from the spot – and Birsent Karagaren followed his team-mate in an early exit.
Tanguy Ndombele then completed the comeback with five minutes to go, though that was unlikely to be enough to prevent significant criticism of Spurs' performance.
Spurs unsurprisingly began on the front foot and went agonisingly close to the lead in just the 10th minute, with Giovani Lo Celso teeing up Bergwijn to hit the frame of the goal from the edge of the box.
Bergwijn was involved again just before the half-hour mark, spinning away from a defender and appearing to be fouled in the box, but no penalty was awarded.
Spurs' dominance continued into the second period, with a lovely move early on again producing a fine opportunity, but Son shot over from around six yards out after Ben Davies latched on to Kane's throughball.
Lo Celso was the next to go close in the 69th minute, curling just past the post from 20 yards, and Lokomotiv capitalised soon after.
Dimitar Iliev flicked on a corner and Minchev nodded in, though much more drama was to follow.
Almeida was given a straight red soon after for handball on the goal-line, while Karagaren was shown a second yellow just a few seconds later after the referee picked up on another indiscretion.
Kane was eventually able to take his kick and made no mistake, before Ndombele slotted home from the centre of the box after being picked out by Lucas Moura.
What does it mean? Questions for Mourinho as Spurs are dominant but unimpressive
Spurs had 77 per cent of the ball across the 90 minutes, as well as 12 shots to Lokomotiv's two – yet they only just managed to scrape an underwhelming result. Lokomotiv's solitary shot on target brought about their goal, while the visitors were so wasteful for much of the game. Son was particularly culpable in that regard, his miss at the start of the second half summing up much of the evening for Mourinho's side, who only scored once their hosts were down to nine men.
Lo Celso shows a bit of class
It is difficult to get particularly excited about any of the performances from the Spurs players here, but Lo Celso certainly was not bad. He created three opportunities, a match-high, shot just wide in the second half and played the joint-most amount of passes in the opposition's half (46).
Son fails to shine
He was certainly involved, but Son will be disappointed with his output. He had just two shots on goal, one of them that bad miss early in the second half, and he failed to make a single key pass.
A trip to Macedonia and Shkendija awaits Spurs next Thursday in the third round of Europa League qualifying. But before then they return to Premier League action at Southampton on Sunday having lost to Everton in their season opener last weekend.