Spurs boss Juande Ramos was forced to field Pascal Chimbonda at centre-half alongside Michael Dawson, with Younes Kaboul ruled out by a groin injury.
Aalborg silenced the White Hart Lane faithful within the first couple of minutes as the Danish side went in front from the first chance of the evening.
Midfielder Thomas Enevoldsen was given far too much time on the edge of the area and he crashed a right-foot shot beyond the despairing dive of goalkeeper Paul Robinson.
The early blow clearly affected Spurs, who took time to get into their stride before Jermaine Jenas started to dominate the midfield.
On the half-hour mark Siyabonga Nomvethe looked set to double the lead, only for Jenas to make a superb recovery tackle on the South African.
However, eight minutes before the break Spurs were 2-0 down as Rade Prica found space on the left and his ball across goal was bundled home from close range by Kasper Risgard.
Ramos brought on Darren Bent and Tom Huddlestone for the second half and within a minute Dimitar Berbatov halved the deficit, as he ran on to Huddlestone's pass to poke the ball home past the advancing Karim Zaza.
Six minutes into the second period it was 2-2 as the Aalborg defence was opened up again and Steed Malbranque crashed home a shot at the far post, despite Zaza getting a hand to the drive.
It was all Spurs now, although Prica continued to offer a threat on the counter for the visitors and just after the hour mark Enevoldsen fired a shot narrowly wide from 20 yards.
With 66 minutes played Spurs went in front for the first time as a Gareth Bale free-kick was only half-cleared and when Aaron Lennon drove the ball back in, Bent was in the right place to score from close range.
More goals looked likely in a highly-entertaining encounter, but none came as Spurs recorded a welcome victory to keep their UEFA Cup hopes on track, with Lennon denied by Zaza in the final minute.