Julius Karangi told reporters that a third soldier was under investigation.
However, he denied there had been "widespread looting" and said there had been an attempt by the media to paint the soldiers as "unprofessional".
Somali Islamist group al-Shabab says it was behind the attack, which killed 67 people over four days.
CCTV footage leaked to local media seems to show soldiers helping themselves to goods in a supermarket in Westgate during the siege.
Gen Karangi has previously said that soldiers had only taken water because they were thirsty but on Tuesday, he said two soldiers had been sacked after being found with items such mobile phones and cameras stolen from the shopping centre.
Army spokesman Col Cyrus Oguna said a local commander had given the soldiers the go-ahead to take snacks from the supermarket.
Gen Karangi added: "There might have been poor judgement on the part of the commander, which is an issue we are dealing with."
Several shop-owners have said that their premises were looted during the siege.
Speaking at the same briefing Gen Karangi, Police Criminal Investigation Department head Ndegwa Muhoro said a phone call had been made to Norway during the siege.
One of the suspected attackers has been named as 23-year-old Somalia-born Norwegian national, Hassan Abdi Dhuhulow.
The Kenyan army has said that all four of the attackers died during the siege which began on 21 September.
Mr Muhoro said that Interpol was helping to analyse the bodies to confirm their identities, reports the AFP news agency.
Officials had initially said there were 10-15 attackers.
Mr Muhoro said that five other people were in detention over the attack and would be charged soon.
Two Kenyan soldiers have been sacked and jailed for looting during last month's attack on the Westgate shopping centre, the army chief has said.