With DPR Korea having already taken the top spot, Iran's hopes of advancing depend on the outcome of all 10 groups, with the best five second-placed sides to also advance to the Finals.
Hong Kong meet Syria in the final group fixture with neither team in a position to qualify.
Despite knowing that their fate was out of their hands, Iran started on the front foot and took the lead through Jordan captain Karzg Shadi Alqasem's 15th minute own goal.
Jordan, already eliminated after suffering three defeats, fought back to draw level through defender Nour Aldeen Amro in the 37th minute with forward Mohammad Mustafa Aburomeh putting them ahead three minutes later.
Iran, however, turned on the power in the second half with defender Abolfazl Kazemi netting the equalizer in the 71st minute.
Strikes from forward Salman Ghafari (77th) and midfielder Mehrdad Agha Mohammadi (90+4, penalty) then confirmed the win, the-afc.com reported.
AMK/TT