It took the visitors until the 75th minute to force a save out of David Button but they built a head of steam and turned a 1-0 deficit into a 2-1 win with goals in the 83rd and 85th minutes.
Earlier, Pekhart confidently dispatched a penalty after Danny Rose was brought down by Daniel Ayala.
Development coach Clive Allen went with a 4-4-2 system, spearheaded by Pekhart and last week's FA Youth Cup goalscorer Alex Olsen. Four of the Academy side that progressed in the FAYC at Southampton started with another four on the bench. The experience was provided by Ricardo Rocha, partnering Dorian Dervite at the back and Wayne Routledge.
It was clear straight away on a bitterly cold evening that the teams weren't treating this a 'friendly' as the ball was pinged about at pace and the tackles snapped in.
Liverpool had a couple of early efforts off target - story of their night until the last few minutes - while we forced the first save of the night as Peter Gulacsi turned away Pekhart's low drive.
The keeper was less convincing from high balls though and there was a decent penalty shout after 22 minutes when he completed misjudged a high ball and flattened David Hutton, but the referee took a lenient view of the challenge.
His next key decision was far more straight forward and led to the opening goal. Joe Martin picked out Rose's run and the midfielder, impressive again, got himself in front of Ayala and would have had a clean strike at goal but for the defender's clumsy challenge. It was a clear penalty and Pekhart did the business, striking the ball into the top corner.
Liverpool finished the half on the front foot but wasted numerous chances - Ray Putterill and Daniel Pacheco took it in turns to blast over from the edge of the area, Dervite somewhat fortuitously blocked Mikel Dominguez's goalbound header and Jay Spearing fired over with an effort closer than Putterill and Pacheco's, but still not troubling Tommy Forecast.
Clive introduced Button, Kyle Fraser-Allen and Yaser Kasim for the second half as half-chances continued to arrive at either end. Pacheco curled just wide, Fraser-Allen's close-range effort was blocked and Cian Hughton got in the way when Ryan Crowther had a sight of goal.
Things warmed up considerably as the game entered its final 15 minutes. First, Button got his angles right to turn away Lindfield's drive and then five minutes later, with 80 on the clock, the save of the night from Gulacsi, fantastic reactions to keep out Pekhart's header from Fraser-Allen's fine cross.
Liverpool kept plugging away and were rewarded in the 83rd minute when Nemeth drilled a free-kick through our defensive wall 20 yards out, Button did well to block but Martin Kelly was left with the easiest of tasks to tap home.
That would have been about right but Liverpool had the last word when Spearing curled a free-kick in from the right and Lindfield planted a header into the top corner from 16 yards.
Defeat was a little harsh, but the purpose of the friendly was more than fulfilled.
Spurs: Forecast (Button, 46), Hughton, Martin, Livermore (Kasim, 46), Rocha (Berchiche, 70), Dervite, Routledge, Rose, Pekhart, Olsen (Hutchins, 70), Hutton (Fraser-Allen, 46). Subs: Cox.
Liverpool: Gulacsi, Kelly, Insua, Dominguez, Huth, Spearing, Crowther, Duran (Ayala, 13), Lindfield, Pacheco (Nemeth, 60), Putterill (Brouwer, 70). Subs: Bouzanis, Bruna, Darby.
Two late goals cancelled out Tomas Pekhart's penalty and secured victory for Liverpool in a highly-competitive reserve friendly at Leyton Orient on Monday night.