Morimoto scored in the 12th and 20th minutes before Guatemala replied through Mario Rodriguez shortly afterwards. Japan, guided by caretaker coach Hiromi Hara as new boss Alberto Zaccheroni still has visa issues to resolve, made six changes from Saturday's 1-0 win over Paraguay.
The hosts started well and went ahead early. Yuto Nagatomo forged down the left flank and Morimoto exploited the space behind the Guatemala defenders to meet the Cesena fullback's cross with a fine header.
Japan doubled their lead in the 20th minute. Shinji Kagawa latched onto a smart pass from Keisuke Honda and fired a shot from close range that was blocked by keeper Ricardo Trigueno, but Morimoto was on hand to tap home the rebound.
Guatemala managed to reduce the deficit just two minutes later. Carlos Castillo stole the ball from Hideo Hashimoto in midfield and quickly fed forward Rodriguez, who displayed neat control before blasting home beyond Japan goalkeeper Seigo Narazaki.
Guatemala midfielder Erwin Aguilar tested Narazaki and defender Carlos Gallardo went close from 25 yards before Nagamoto saw an effort fly just wide after cutting into the box from the left. Second-half substitutions disrupted the rhythm of the game but Hashimoto threatened the Guatemala goal in the 77th minute and two minutes later defender Mitsuru Nagata headed over the bar.
Guatemala substitute Minor Lopez could not beat Narazaki with a mid-range drive in the 80th minute as the two sides were unable to add to the scoreline.
Iran gave their preparations for January's Asian Cup a massive boost with a 1-0 friendly win over Korea Republic. Osasuna star Masoud Shojaei scored after 35 minutes to inflict the first defeat for the Taeguk Warriors on home turf since January 2008. For Iran, it was their second win in four days following a 2-0 triumph over China.
Lee Chung-Yong and Park Ji-Sung went close early in the match but 10 minutes before the break, their team fell behind as Shojaei gave the visitors the lead following a mistake from Lee Young-Pyo.
The full-back gave the ball away in the centre circle to allow Pejman Nouri a run on goal and the Malavan midfielder squared the ball to Shojaei on the edge of the area, who clipped the ball over advancing keeper Jung Sung-Ryeong.
Korea Republic piled on the pressure in the second half but struggled to penetrate a stubborn defence and found Mehdi Rahmati in fine form when they did. The Sepahan goalkeeper pulled off a superb reaction save to deny Park Chu-Young from close range with 15 minutes remaining.