Afshin Ghotbi this time went for a 4-3-3 formation, however, whatever hopes he had put in the system switch, were disappointed by uninspired, yet dominant, first half performance by his team.
Ghotbi brought Mohammad-Reza Khalatbari for Pejman Nouri for second half, switching back to the usual 4-2-3-1 and immediately Iran created much more danger than before the interval.
Karim Ansarifard (53'), Javad Nekounam (55') and Masoud Shojaei (62') failed to break the deadlock, before finally Nekounam once more came to rescue Team Melli.
27 minutes into second half the Osasuna midfielder got to the end of an Andranik Teymourian cross from the left and perfectly headed the ball into the net from close range.
Things turned from bad to worse for the visitors, when the already booked skipper Mohammad Shelbaye received his marching orders for a foul on Khosro Heydari.
Iran created several opportunities to double the lead, but Ansarifard (78'), substitute striker Farhad Majidi (81') and Teymourian (81' / 85') only came close to add their names to the scoresheet.
The biggest chance came in the final minute of the game, when Majidi, who had brought some fresh air into Iran's attacking game after replacing the today disappointing Masoud Shojaei, set up the also convincing Mehrzad Madanchi, who's shot could only be blocked by the goalkeeper and Ansarifard smacked the rebound against the goalpost from short distance.
Jordan only once came close to an equalizer, when a confusion in Iran's defense almost lead to an owngoal by Nosrati, but the ball rolled past the post.
Iran will host Macedonia in a friendly match on Wednesday, before again facing Jordan in Asian Cup qualification in Amman on Sunday.
Iran - Jordan 1-0 (0-0)
Asian Cup Qualification, Azadi Stadium, Tehran
Goal: 1-0 Nekounam (72' / Assist by Teymourian)
Iran: Rahmati - Heydari (88' Kaebi), Aghili, Nosrati, Hajsafi - Teymourian, Nekounam, P. Nouri (46' Khalatbari) - Shojaei (66' Majidi), Ansarifard, Madanchi
Iranian players booked: Madanchi
Suspension: Shelbaye (second yellow / Foul / 73')