With the game heading towards a draw, Suarez broke clear and fired past Hart to seal the points for his side.
Here, Sports Mole takes a closer look at the events that unfolded at the Arena Corinthians.
On Target 2
On Target 6
Was the result fair?
In the end, a defeat was harsh on England. Roy Hodgson's men were largely in control of the match and enjoyed sustained periods in possession. From the start they seemed the side more likely to take the lead and Rooney in particular was unlucky not to find the net in the first half. A lack of clinical finishing proved to be the difference as Uruguay only had two attempts on target and scored twice.
Uruguay were not at their best, but performed far better than they had done against Costa Rica. Their defence was solid throughout the evening and very rarely were England able to get in behind. Despite seeing far less of the ball, they were able to break quickly and make good use of the chances that fell their way. They were lucky not go down to 10 men when Diego Godin appeared to foul Raheem Sterling, having already picked up a yellow card. It was a contentious moment and came at a time when the scores were level. Their forwards made the difference tonight, as Edinson Cavani and Suarez combined brilliantly for the first goal, with the Liverpool forward adding a stunning late second.
Despite putting in decent displays in both of their opening group games, England are on the verge of exiting the tournament. Rooney was finally able to break his goalscoring drought at the World Cup and produced a far more impressive performance in a familiar central role. Daniel Sturridge and Sterling were busy in the attack, but were unable to make a huge impact on the proceedings. It was in defence where England were found out again, as Gary Cahill and Phil Jagielka failed to cut out the runs of Suarez for his goals. There are certainly positives to take, but Hodgson will be disappointed that his team could not hold out for a point, with their tournament hopes hanging by a thread.
Sports Mole's man of the match
Luis Suarez: The Liverpool forward was exceptional this evening, as he made his return from injury. He did not play in the defeat against Costa Rica, but started with his country in need of a result this evening. Even if he was not fully fit, he took his goals brilliantly and made England pay in the cruelest fashion. His late strike past Hart was taken emphatically and if he stays fit for the rest of the tournament, then there is no telling how far the Uruguayans can go.
Godin should have been sent off for Uruguay less than 30 minutes into the match. He had already picked up a booking for an early handball and should have seen another yellow card for a foul on Sterling. Gerrard's poor header back to his own goal that set up Suarez to run through and score is also a moment that England will want to forget.
Carlos Velasco Carballo only handed out two yellow cards in a match that saw a number of poor challenges from the Uruguay team. He should have sent off Godin, but allowed him to stay on the pitch following what looked like a certain second bookable offence.
Uruguay: Uruguay face Italy in their final group match in Natal next Tuesday.
England: The Three Lions are also in action on Tuesday and take on Costa Rica in Belo Horizonte.