Dublin, Ireland – Steven Pienaar, Andros Townsend and Jermain 0 win over Shamrock on Thursday, but the English side was still eliminated from the Europa League.
Tottenham finished Group A with 10 points, trailing Greece's PAOK and Russia's Rubin, which secured second place with a tie at PAOK on Thursday despite being down a man for nearly 80 minutes.
PAOK finished atop the group with 12 points, followed by Rubin with 11. Spurs, which could have joined Manchester City and Manchester United in the last 32, would have advanced if Rubin lost to PAOK.
Harry Kane added a fourth goal in the closing minutes at Tallaght Stadium for Tottenham, which can now focus on maintaining its top-four spot in the English Premier League.
PAOK put Tottenham in good position early when Vieirinha converted a penalty - which resulted after Sergei Ryzhikov was sent off - but 10-man Rubin pulled a goal back early in the second half and held on for the draw.
Shamrock finished group play with six losses in as many matches.
In Group B, Konstantin Rausch and Didier Konan scored in the opening half and Hannover defeated Vorskla Poltava 3-1 to follow group winner Standard Liege, which wrapped up an undefeated group stage with a 1-0 win over FC Copenhagen, into the knockout round.
Michy Batshuayi scored on the half-hour mark for Standard Liege, which managed four wins and two draws in group play to finish with 14 points. Hannover ended with 11 points to finish second.
In Group C, Stanislav and Tim Matavz scored and PSV Eindhoven ended group play unbeaten with a 2-1 win over Rapid Bucharest and Salim Toama and Avichai Yadin scored as Hapoel Tel-Aviv picked up a 2-0 win over Legia Warsaw, which already had clinched advancement along with PSV.
PSV won five of its six games to finish with 16 points. Legia finished second with nine points.
In Group G, Adam Maher answered Marko Devic's goal in less than 60 seconds, as AZ Alkmaar tied group winner Metalist Kharkiv 1-1 to hold off Austria Vienna for second place and a spot in the knockout stage.
Metalist previously clinched the group, but AZ needed the draw to finish level on points with Austria Vienna, which downed Malmo 2-0, to advance to the final 32 on a tiebreaker. Malmo finished last without a win.
In Group H, Ewerton scored as 10-man Braga notched a 1-1 draw against Club Brugge that sent both clubs into the knockout stage. Uwa Echiejile was sent off after 15 minutes, but Ewerton answered Bjorn Vleminckx's goal to save Braga.
Adam Rooney fired Birmingham City to a 1-0 win over winless Maribor, but the English side ended third with 10 points to finish one point off both Brugge and Braga. Brugge finished first on a tiebreaker.
In Group I, Antonio Di Natale scored as Udinese tied Celtic 1-1 to secure its place in the last 32 at the expense of the Scottish side. Gary Hooper put the Bhoys in front, but Di Natale equalized to help Udinese secure second.
Falcao opened the scoring as group winner Atletico Madrid finished with a 3-1 win over winless Rennes.
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