Despite a bright start by an experimental England lineup, Walter Ayovi's cross from the left-hand side was powerfully headed home by Enner Valencia, only for Rooney to bundle home before the halftime after Lambert's close range flick came back off the post.
Roy Hodgson's side began the second period in the ascendancy, and Lambert was on hand to drive his team into the lead, after Ross Barkley's fine run from midfield set up a chance for the new Liverpool striker on the edge of the area.
That goal sparked the South Americans back into life, and after Valencia struck a post, substitute Michael Arroyo fired into the top corner from 20 yards as England defenders stood off.
Both teams looked to make substitutes late on, though the game ended in some controversy as Raheem Sterling and Antonio Valencia were both given their marching orders in the closing stages.
Despite the fact that England started with plenty of attacking intent - Frank Lampard missed the target with a side-footed effort following Lambert's drag back - Hodgson's experimental side was left shell-shocked by Valencia's eighth-minute opener.
Walter Ayovi superbly controlled an aerial ball on Ecuador's left flank before crossing for the forward to sneak in between Chris Smalling and Luke Shaw and steer a firm header beyond Ben Foster, making his first start for his country since November 2010.
Nerves appeared to be getting the better of Foster when he scampered out and failed to win the ball soon after during a swift Ecuador counter, but the West Brom goalkeeper eventually got back on his line and gathered comfortably to collect Carlos Gruezo's weak curling shot.
Lampard let fly from 25 yards to test a sprawling Maximo Banguera after 24 minutes, but England did find the net five minutes later.
Oxlade-Chamberlain sent a delicate chip to the back post as Lambert lurked ominously, although the new Liverpool striker appeared to control the ball with his arm before his close-range backheel rebounded off the post and ricocheted off Banguera to Rooney.
The Manchester United striker, deployed on the left of midfield, duly slotted home his first England goal since October last year and, more significantly, netted a strike that will boost his confidence as he battles to regain full fitness after an injury-blighted end to the season.
Barkley, keen to catch the eye on his first England start, combined brilliantly with Lambert six minutes into the second half to give England the lead.
The Everton youngster nutmegged Jorge Guagua at the start of a jinking run that ended when he rolled the ball into the path of Lambert, who crashed a low effort across Banguera with the outside of his right foot.
Lambert came close to doubling his tally four minutes later after good work from Oxlade-Chamberlain, while at the other end, Enner Valencia somehow managed to hit the post with the goal at his mercy.
Arroyo then made his spectacular impact within a few minutes of his introduction as he moved the ball quickly at his feet to find space ahead of James Milner and Jack Wilshere before rifling into the top-right corner from 25 yards.
Then, with 12 minutes left, substitute Sterling and Valencia clashed in an unsavory incident that both players will want to move quickly on from with the World Cup looming.
Valencia took exception to a challenge from Sterling and grabbed the Liverpool winger by the neck, although fortunately for the pair they will be clear to play in the Brazil showpiece.
Next up for England is a friendly with Honduras in Florida on Saturday, while Ecuador will head to Brazil in buoyant mood after causing Hodgson's men plenty of problems.