The weekend attacks will again prompt questions about the extent to which the Islamic State group affiliate is a spent force, as Nigeria's government has claimed.
There was no official claim of responsibility but the attacks bore the hallmark of Boko Haram, which has frequently hit checkpoints and security services with suicide bombers.
Rebel fighters, whom the military said were ousted from their Sambisa Forest enclave in Borno state last month, first hit an army base in Buni Yadi in neighbouring Yobe state, at dusk on Saturday.
One senior officer, speaking on condition of anonymity as he was not authorised to talk to the media, said the Buni Yadi assault led to an "intense battle".
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"We lost five soldiers in the attack, including a captain who was recently deployed to Buni Yadi," he said. "We are still trying to have a sense of the casualties on the part of the terrorists as their bodies are scattered in the bush."
The Boko Haram gunmen are believed to be remnants of those flushed out of Sambisa as a result of a sustained military operation that began in April last year.
Attacks on military bases were a regular feature of the fighting and used by Boko Haram to replenish weaponry.
A spokesman for the Buni Yadi base, Lieutenant George Okupe, confirmed the attack and said it was "repelled". He said: "I cannot confirm any casualty for now. All I can say is that some soldiers are missing in action."
Buni Yadi, some 65 kms from the Yobe state capital, Damaturu, fell into the hands of Boko Haram in February 2014 after the militants attacked a boys' boarding school.
On Sunday at about 10:30 pm (2130 GMT), two female suicide bombers killed two people in the Kaleri neighbourhood of Maiduguri, said Borno state police spokesman Victor Isuku.
Civilian vigilante Babakura Kolo and local residents said the targets were the homes of militia members helping the military in the area.
The first bomber was aged about 20 and killed both herself and the vigilante member's teenage daughter, who answered the door.
The second female bomber was believed to be aged about 30 and killed the father of the vigilante, who was spending the night with his second wife, said resident Bura Kadiri.
"The IED (improvised explosive device) strapped to their bodies exploded, killing all of them, and a civilian JTF," said police spokesman Victor Isuku.