Peseiro used the same starting line-up that lost 2-1 to Mexico.
Villarreal full-back Pervis Estupinan ghosted the Super Eagles' defenders to connect with a free-kick to head past goalkeeper Francis Uzoho.
Nigeria denied a penalty in the 13th minute after Terem Moffi, from a pass from Alex Iwobi, seemed to have his leg taken by the Ecuador goalkeeper Alexander Domínguez but the referee and his assistant agreed it was not a foul despite vehement complaints from the Nigerians.
Uzoho made a diving save from a Jose Cifuentes curler in the 21st minute. Another defence-splitting pass from Iwobi presented a goal-scoring chance to Cyriel Dessers but Domingues made a good save. From the resultant corner, Semi Ajayi had a header saved before Moffi poked wide.
Peseiro introduced Ola Aina and Emmanuel Dennis in the second half alf to replace Awaziem and Faisal with the Watford forward missing a chance in the 58th minute.
At a point the match was filled with whistles as both sides committed fouls.
Peseiro sent on Victor Mbaoma for Moffi in the 85th minute and Uzoho made a fingertip save from Jeremy Sarmiento’s goal-bound shot in the 88th minute as the Ecuadorians attacked after being put under a lot of pressure by the Eagles.
Four minutes were added on but the Eagles could not find the equaliser.
Peseiro lost his second game in charge and will be keen for a first competitive win on June 9 against Sierra Leone in a Nations Cup qualifier.