Sir Michael Fallon wrote to a number of families apologising for delays in bringing in alternative protected vehicles "which could have saved lives".
At least 37 UK soldiers died in conflicts in Iraq and Afghanistan while travelling in Snatch Land Rovers, with last year's Chilcot Inquiry heavily critical of delays in replacing them.
"I am fully aware of the struggle you have had to bring this matter to court over the last decade and I recognise this has had a significant impact on you and your family," Sir Michael wrote in his letter to the families.
"The Government entirely accepts the findings of Sir John Chilcot in the Iraq Inquiry in relation to Snatch Land Rover.
"I would like to express directly to you my deepest sympathies and apologise for the delay, resulting from the decisions taken at the time in bringing into service alternative protected vehicles which could have saved lives.
"I confirm that we have learnt lessons from this.
"The Government must and will ensure that our Armed Forces are always properly equipped and resourced."
The letter comes after a lengthy legal battle, which eventually saw the Supreme Court rule the families could bring compensation claims against the Government under legislation covering negligence and human rights.
Sue Smith's son, Private Phillip Hewett, was killed whilst driving a Snatch Land Rover in Iraq in July 2005.
Pte Hewett had told his mother he was driving a Warrior tracked armoured vehicle rather than the Snatch, so that she would not worry.
Prior to this, Pte Hewett had written to his uncle saying some soldiers had purposely lost their driving licences so they would not have to drive the Snatch.
Ms Smith criticised the MoD's conduct during her legal case, saying a lot of information it said was unavailable or too difficult to provide had already be handed over to Chilcot.
"Never for one minute did I think my family would be treated in this way," she said.
"I feel that the MoD have been dishonest in their dealings with me and have put me through a great deal of unnecessary stress in continuing to fight this case.
"I think they wanted to break me so that I would walk away but, it only made me more determined to fight on."
Private Lee Ellis was killed in Iraq in February 2006, and his sister Karla Ellis said the explanation she received about his death "never made sense".
She added: "What has been achieved is beyond my wildest dreams and I am so grateful that I've been able to honour my brother's memory in this way.
"It's been the longest of journeys but we have shown what can be achieved if you're prepared to fight."
The families' lawyer, Jocelyn Cockburn, has also received a letter from the Ministry of Defence confirming it had learnt lessons from Chilcot and was also procuring the next generation of armoured vehicles.
"This is an important victory for the Snatch Land Rover families, who have had to fight every step of the way to achieve justice," Ms Cockburn said.
"The Ministry of Defence's stance of 'delay, deny and defend' has caused untold suffering to already grief-stricken families over a needlessly long period.
"However, I am relieved that their battle is over and genuinely hope that their apology signals a sea-change in the way the MoD seeks to deal with bereaved service families."
General Sir Mike Jackson, Chief of the General Staff between 2003 and 2006, told BBC Radio 4's Today programme it was a fair assumption that a more heavily armoured vehicle would have offered much better protection for British troops.
He said he believed replacements for the Snatch Land Rover could have been brought in more quickly, adding: "The Army at that point did not have its own procurement budget.
"It does now, and perhaps that is one of the good lessons learned that's come out of this whole rather sorry story, we do have our own procurement budget now.
"Yes, better vehicles, better-protected vehicles were eventually procured, but the process was rather Byzantine and inevitably, thereby, lengthy."
An MoD spokeswoman said: "We offer our deepest sympathies and apologise for the delay in bringing into service alternative protected vehicles which could have saved lives.
"The Government acknowledges and fully accepts the findings of Sir John Chilcot's inquiry in relation to Snatch Land Rovers.
"Our Armed Forces now use a number of highly capable and extremely well protected patrol vehicles, including Mastiff, Ridgback, Husky and Wolfhound."