Sri Lanka will play three one-day internationals in Karachi and as many T20Is in Lahore between September 27 and October 9, a statement from the Pakistan Cricket Board (PCB) said.
According to the original programme, Pakistan was scheduled to host Sri Lanka for two World Test Championship matches in October before Sri Lanka returns for three ODIs and three T20Is in late December.
The decision to swap matches was made following a aphone discussion between PCB Chairman Ehsan Mani and SLC President Shammi Silva on Friday, the PCB said in a statement.
The Sri Lanka cricket team will arrive in Karachi on September 25 where it will play three ODIs on September 27 and 29 and October 2.
Lahore will host three T20Is on October 5, 7 and 9 after which the visitors will fly home on 10 October, the statement read.
PCB Chairman Ehsan Mani said: "The PCB is pleased with the outcome of its discussions with Sri Lanka Cricket, which has supported Pakistan in its efforts and endeavours for the complete revival of international cricket. The tour for limited overs matches will also provide Sri Lanka with an even better understanding of the ground situation before discussing schedule of the Tests.
"The upcoming matches will end the long await of the Pakistan cricket fans and supporters to watch modern day stars from both sides live in action. This is something that will contribute immensely to our revamped domestic cricket structure.
"The hosting of the ICC World XI, a T20I against Sri Lanka, three-T20I series men's and women's series against the West Indies and eight HBL PSL 2019 matches within the past couple of years is a testament to Pakistan's claim that it is a safe and secure country to play cricket.
"We are very grateful to Sri Lanka Cricket President Mr Shammi Silva, his board and players for responding positively to our request to play matches in Pakistan.
"The PCB looks forward to welcoming the Sri Lanka cricket team and assure them that they will be as well looked after as any other international sides of the past."
SLC President Shammi Silva said: "The PCB and SLC have a long history of cricket relationship and friendship, and this decision only strengthens that bonding. The SLC is committed to playing its role in the promotion of cricket and looks forward to visiting Karachi and Lahore for three ODIs and three T20Is.
"The SLC security experts had visited the two cities earlier this month and had given a positive report, which made our job of decision-making easy.
"The safety and security of its players is the responsibility of the SLC, which it takes very seriously. If there had been any doubts, the SLC would not have gone ahead with this arrangement that we envisage will improve the players' confidence and trust level and will also be critical when we start discussions on the schedule of the Test matches."