Roy Hodgson's side looked set for a shock defeat after Ukraine midfielder Yevhen Konoplyanka produced a sublime strike to open the scoring in the first half.
But Lampard had netted twice in Friday's 5-0 win over Moldova and the 34-year-old was back on the scoresheet in the nick of time as he converted another spot-kick after Yevgen Khacheridi's 85th minute handball.
While Hodgson will have been relieved to see his side preserve their unbeaten start to the qualifying campaign, this was a worrying night for the England coach.
For he will be without captain Steven Gerrard for the next qualifier against San Marino after the Liverpool midfielder was sent off in the final moments for a second booking.
Hodgson insisted England had done enough to merit a draw.
"The first 15 minutes we weren't at our best. The next 75 minutes we dominated the game.
"The fact is we played against a very good Ukraine team but I was very pleased with the way the players went about their task.
"We created chances and struck the post three times. We thoroughly deserved a point."
Britain may be enjoying a golden period of sporting success at the moment, but the feelgood factor from the country's Olympic triumphs and Andy Murray's US Open victory clearly hadn't made it to Wembley, where vast swathes of empty seats provided an uninspiring backdrop to Hodgson's first competitive game on home turf.
Oleg Blokhin's team had almost taken an early lead when Oleg Gusev's cross deflected off Alex Oxlade-Chamberlain and looped over Joe Hart before glancing off the far post.
Hodgson's side needed a goal to quell Ukraine's confident start and they thought they had it when Jermain Defoe cut in from the left to lash a powerful strike past Andriy Pyatov in the 10th minute.
But Turkish referee Cuneyt Cakir ruled out the goal, claiming Defoe had fouled Andriy Yarmolenko with an arm to the throat, even though the Ukraine forward seemed to exaggerate the minimal contact.
With John Terry sidelined by an ankle injury, Hodgson had picked Phil Jagielka ahead of Gary Cahill at centre-back, but England looked ponderous in defence and Gerrard had to clear Ruslan Rotan's low shot off the line after another incisive Ukraine move.
But England should have been ahead 10 minutes before half-time.
Gerrard whipped a cross towards Defoe, who headed across goal to the unmarked Tom Cleverley. Yet, with just Pyatov to beat from six yards out, Cleverley somehow contrived to shoot straight at the Ukraine goalkeeper.
Cleverley held his head in frustration and England's misery deepened in the 39th minute as Ukraine took the lead in stunning style.
After Joleon Lescott conceded possession with a careless pass, Ukraine worked the ball across midfield to Konoplyanka, who cut in from the left, took aim from 25 yards and fired a superb curling strike past Hart.
With England showing little sign of breaking down the Ukraine rearguard, Hodgson sent on Danny Welbeck in place of Cleverley and Daniel Sturridge for Oxlade-Chamberlain.
That finally added some zest to England's attack and Glen Johnson's low strike brought a fine save from Pyatov before Welbeck hit a post from close-range.
To their credit, England kept plugging away and they equalised five minutes from the end.
Khacheridi conceded the penalty when he blocked Welbeck's flick with his arm and Lampard stepped up to drive home the spot-kick.
However, there was still time for Gerrard to be dismissed for a rash lunge on Denys Garmash as England finished on a suitably downbeat note.