The incident proved decisive because up until then United had been thwarted by Bolton keeper Jussi Jaaskelainen.
The Bolton keeper made decent saves from Frank Lampard and Florent Malouda.
It was no less than Tottenham deserved, despite their nerves, with Bolton keeper Jussi Jaaskelainen saving from Gareth Bale and Peter Crouch twice.
The home side started well, forcing returning Bolton keeper Jussi Jaaskelainen to slice the ball out for a throw-in with just seconds gone.
Birmingham came close to equalising when Heskey raced through to test Jaaskelainen with a cleanly-struck effort, but the Bolton keeper stood up well to make the block.
Tony Hibbert's hanging cross led to a mix-up between Bolton keeper Jussi Jaaskelainen and Tal Ben Haim and Cahill's athleticism allowed him to fire home an overhead kick from close range.
There could have been late drama when Sami Hyypia's mistake gifted the ball to Dave Edwards in the Finland box but Bolton keeper Jaaskelainen reacted quickly to deny him and Wales who will finish fourth in the group.
The Portugal international then tried his luck from the opposite side and this time the Bolton keeper could only parry the ball back into the path of Berbatov, who poked home to give United what could prove to be a vital three points.
The in-form Gareth Bale was again the hosts' most threatening attacking outlet, the winger forcing a smart save from Bolton keeper Jussi Jaaskelainen from range, while Roman Pavlyuchenko should have done better from one of the Welshman's crosses from six yards out early on.
It was credit to Bolton's defence that their keeper Jussi Jaaskelainen was rarely called into action.
But they might want a more assured display in Manchester after a professional Bolton display ran them close in this game - and a late injury worry over keeper Gomes will have to be assessed before Wednesday too.
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