NWAS lost the contract, now worth £66.8m, to bus operator Arriva in 2013.
Arriva withdrew from the new tendering process after admitting providing false data about its current performance.
NWAS was also awarded similar five-year deals for Lancashire, Merseyside and Cumbria, but lost the Cheshire tender to West Midlands Ambulance Service.
A spokesman for NHS Blackpool Clinical Commissioning Group (BCCG), the lead ambulance commissioners for the North West, said Arriva had "identified a level of management failure with the reporting of performance in Greater Manchester" in October.
"This means that they had previously provided incorrect information, which shows a higher level of performance than is the case," he said.
He added that following Arriva's admission, the company "withdrew from the procurement process immediately" and has "since developed a performance improvement plan to help rectify their performance".
NWAS chief executive Bob Williams said that while he was pleased to regain the Greater Manchester contract, it was "tinged with disappointment" because of the loss of the Cheshire, Warrington and Wirral service.
"Whilst we were successful in four of the North West's counties, our immediate focus now is on our staff in Cheshire and the impact on them," he said.
"We will work closely with our trade unions, staff and the new provider to support them through this period and deliver a safe and smooth transition."
The BCCG spokesman said the contracts had been awarded as "the result of a rigorous competitive tendering process and evaluation of potential providers".
He said the new NWAS contracts would see "a number of quality improvements", including a "text-ahead service" to inform patients when their transport will arrive and a "revised process" to ensure fair use of the service.
The new five-year contracts - worth £59.9m in Lancashire, £39m in Merseyside, £31.5m in Cumbria and £24.6m in Cheshire - will begin in July 2016.
The North West Ambulance Service (NWAS) has been restored as the provider for non-emergency patient transport services across Greater Manchester.