Town couldn't build on a swashbuckling first-half performance as they all but surrendered to Rovers with a timid showing after the interval.
The visitors went ahead in stunning style in just the second minute with Lambert's goal-of-the-season contender; a brilliantly executed volley from 30 yards out.
It was all Hatters after that, but they could only force an equaliser amid farcical circumstances in the 19th minute after referee Fred Graham ordered Matt Spring to take his penalty three times before he finally registered his third goal of the season.
Rovers finally came out on the offensive after the break and, after several close-calls for tired-looking Town, Lambert put Luton to the sword by heading home the winner in the 82nd minute.
As expected Hatters rang the changes again after their 2-0 midweek Johnstone's Paint Trophy win over Northampton.
Back came Cardiff loan man David Forde in goal, skipper Chris Coyne, Richard Jackson, Spring, Darren Currie and Paul Furlong.
Dave Edwards was missing after playing in Wales Under 21s' 1-0 defeat to France on Friday night.
Rovers, with their director of football, former Luton manager Lennie Lawrence taking his place on the bench, handed a first start of the season to ex-Hatters loanee Sammy Igoe with Joe Jacobson absent having also having played in the Welsh Under-21 defeat.
The game had an early noon kick-off, but took no time to warm up as the visitors went ahead after just 67 seconds in sensational fashion.
Rovers keeper Steve Phillips punted a routine clearance upfield and, after Coyne and Andrew Williams challenged, the ball dropped to Lambert who hit an instant volley from 30 yards that rocketed past Forde into the top corner for a truly superb goal.
Luton were not rattled though and playing slick, one-touch football, with David Bell prominent, they fashioned openings for Furlong to chip just over in the fourth minute and Coyne to head at Phillips two minutes later.
More probing from Bell led to Hatters winning a penalty in the 16th minute when Furlong fell under Byron Anthony's challenge after a pass from the ex-Rushden man.
But astonishing scenes then saw Spring forced to take his spot-kick three times before registering Town's leveller.
First he blasted high to Phillips right only for the effort to be disallowed for encroachment from Drew Talbot.
Then he went the other way, firing low to the goalkeeper's left-hand corner, only for referee Graham to order yet another re-take with Currie this time appearing to be the offender in running into the area too soon.
Spring held his nerve to net for the third time in succession, going back to Phillips' right, with the goal eventually being registered in the 19th minute.
From then on it was all Luton, with the Town displaying some breathtaking cross-field passing.
However, with Rovers' massed ranks protecting their goal, all Hatters could manage was a 25-yard Spring effort at Phillips in the 39th minute - and that came after Lewis Haldane had fired over from 20 yards five minutes earlier in a rare attack from the visitors.
For all their first-half possession, Town had failed to create openings, but a chance came along just five minutes after the break as Currie - who had switched flanks with Bell - crossed from the left and Coyne, up from the back, headed across goal for Furlong to nod wide on the stretch from six yards.
Luton then lost their way as Bristol Rovers ventured forward with Igoe smashing a 20-yarder wide, Steve Elliott having a header cleared off the line from Currie after Stuart Campbell's corner, Lambert heading just wide from another Campbell flag-kick and the same player then firing over from 12 yards after Haldane's cross – all in the space of ten minutes.
Hatters couldn't regroup and, with Alan Goodall regularly being caught in possession, the visitors came again.
Craig Disley fired just off target in the 72nd minute before Forde twice had to come to Luton's rescue in the space of 60 seconds, saving smartly from Elliott and Lambert in the 81st and 82nd minutes after two Campbell corners had caused mayhem in the home area.
It was another Campbell corner that undid Luton as Lambert rose highest to head home at the far post for the winner eight minutes from time.
Substitute Paul Peschisolido went close when his ten-yard shot was cleared off the line by Anthony after Coyne had challenged Phillips in the final minute, but Luton couldn't force an equaliser.