State media on Wednesday described the attack as a "provocative action" by Maj. Gen. Ali Mohsen al-Ahmar, commander of the 1st Armored Division, that had to be quelled by the government's rapid response forces.
"The leader of the 1st Armored Division is responsible for any attempts that could cause security tensions," the government statement said, raising the tensions between the two long time rivals.
Yemen's military split on March 17, when President Ali Abdallah Saleh's chief competitor for power, al-Ahmar, abruptly declared his solidarity with the protesters who have been demonstrating for weeks calling for the president's ouster.
The move presented the unsettling possiblities of two well-equipped militaries stationed in the capital battling it out. Until Tuesday night's incident, there had been no clashes.
Yemen has been wracked by protests since mid-February over the country's lack of freedoms and its extreme poverty. More than 120 people have been killed since the uprising began on Feb. 11, inspired by popular uprisings in Tunisia and Egypt.
In the southern capital of Aden, security forces clashed on Wednesday with thousands of protesters who hurled rocks and burned tires, killing at least one person.
The army and anti-riot police, backed with tanks and artillery, fired live ammunition and tear gas in Aden, according to eyewitnesses. Medical officials said one person was killed and seven wounded.
Tens of thousands also demonstrated in the capital Sanaa in some of the biggest demonstrations to date for this impoverished nation that is already plagued by dwindling supplies of food, water and oil.
Until recently, U.S. officials have expressed a degree of measured support for Saleh, though that has been ebbing in the face of the overwhelming popular opposition to his continued rule across the country.
Saleh is a close U.S. ally in the fight against al-Qaida and a local franchise of the organization has taken root in Yemen's lawless hinterlands, plotting several unsuccessful attacks against America.
Late on Tuesday, plainclothes gunmen armed with heavy machine guns bolted on vehicles attacked the checkpoint north of the capital controlled by al-Ahmar's men.
Local residents said they heard the sound of explosions, gunfire and saw flames shooting into the sky. Military officials say the attackers were members of the Republic Guard and military police loyal to the president. Both residents and officials spoke on condition of anonymity because of the sensitivity of the issue.
The checkpoint guards the way to the northern province of Imran, a bedrock of support for al-Ahmar and may have been an attempt to stop more anti-government demonstrators from flowing into the city.
If al-Ahmar's forces attempt to extract revenge for the attack, Yemen's popular uprising could turn into a Libyan-style all out war, except with two evenly matched sides armed to the teeth with modern weapons.
Saleh has offered to step down at the end of this year if an acceptable transfer of power is reached, but the opposition fears he is just stalling for time.
The six-nation Gulf Cooperation Council offered its own proposal Sunday to end the unrest and called on Saleh to transfer power to his deputy as part of a deal with the opposition. The deal did not, however, specify a timeframe and included immunity from prosecution for Saleh and his family.
The opposition Civil Alliance of the Youth Revolution, which includes 30 youth groups, rejected the proposal.