After giving up a goal to Chancel Mbemba's header in a tense first half, Tottenham appeared to be advancing to the Europa League.
However, after the break, they played better, allowing Clement Lenglet to equalize and Pierre-Emile Hojbjerg to steal the victory at the very last second to guarantee their place in the round of 16. This was their first triumph in Europe away from home in eight matches.
It seemed appropriate that qualifying was decided so late given that their destiny depended on the outcome of the last group game following last week's VAR intervention versus Sporting Lisbon.
Tottenham knew defeat would eliminate them, so the entire 90 minutes were packed with danger. However, victory ensured Spurs advanced to the knockout stages for the fourth time in a row in this competition, and they will play a second-place team when it restarts in 2023.
There was a sense of certainty about how the match began considering Spurs' struggles on the path in Europe and Marseille, with three ex-Arsenal players in their side, were quickly out of the doors speedily. This was never going to be simple, particularly with Antonio Conte restricted to the stands due to a touchline ban.
Within the first five minutes, Alexis Sanchez had a chance to put them in front, but he narrowly missed Amine Harit's cross.
The former Arsenal player, who scored three goals against Tottenham hotspur while playing in England, appeared to be Marseille's most dangerous player. He put Hugo Lloris to the trial with a shot on the spin, but the France goalie deflected it away to keep Marseille out in the game.
Spurs may have been waiting for their opponents to make a mistake, but they lost a crucial piece of that strategy on the half-hour when Son Heung-min was taken off following a hard clash with Mbemba.
The South Korean left with a bleeding nose and came out extremely unsteadily, therefore he might not play against Liverpool on Sunday due to potential concussion protocols.
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Lloris, who was the busiest player for Spurs, made a diving save to stop a ferocious effort from Jordan Veretout that was aimed for the top corner.
But ultimately Marseille's pressure paid off, and they scored in the final seconds of the first half.
Due to Ryan Sessegnon's error, Marseille swiftly took a corner, and Mbemba easily headed the ball home at the far post.
Having still not performed a forward pass in Marseille's half, Tottenham were hopeless, but they came out in the second half and instantly responded, tying the scoreline in the 54th minute.
Lenglet headed home a superb free kick from Ivan Perisic as Spurs maintained their supremacy at set pieces.
Conte's team was starting to find space as the game opened up, and there were a few opportunities for them to gain the upper hand.
They missed an opportunity to counter when Lucas Moura's through ball was overhit by Rodrigo Bentancur. Spurs recovered the ball, but Harry Kane was unable to tap in when Emerson Royal's cross was spilled by Pau Torres.
They believed their chance had arrived in the 80th minute when Hojbjerg's attempt from 14 yards hit the crossbar after they executed a throw-in beautifully with the help of Bentancur and Moura.
A minute later, Kane had a clear shot at goal but Mbemba made a wonderful last-ditch tackle to stop him just before he could fire.
Sead Kolasinac, a former Arsenal player, missed a free header at the far post in the 87th minute, giving Tottenham a fright.
With a tie, it appeared like the game would be over, but Spurs ensured victory when Kane found Hojbjerg, who scored forcefully to quiet the boisterous Marseille supporters.
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