The two agents did not report the shooting to their superiors and tried to cover up the incident but their convictions drew sharp criticism from advocates of tough US border security policies who said they were just doing their jobs.
The agents will still face three years of supervised release and a $2,000 fine, but will not be released on March 20.
A White House official who asked not to be named said this was expected to be Bush's last act of clemency before his presidency ends at noon (17:00 GMT) on Tuesday when Barack Obama takes office.
The two commutations were in marked contrast to predecessor Bill Clinton, who issued a flurry of 140 pardons on his last day as president.
Controversy still reverberates over Clinton's last-minute pardon of fugitive financier Marc Rich, whose ex-wife was a major Democratic donor.
Obama's choice for attorney-general, Eric Holder, faced questions about the Rich pardon during confirmation hearings and said he erred in supporting the 2001 pardon when he was Clinton's deputy attorney-general.
Clinton issued 396 pardons and commuted 51 sentences in his two terms as president while Bush's father, who preceded Clinton, issued 74 pardons and commuted three sentences in his four years in office.
Bush issued 189 pardons and 11 commutations of sentences during his eight years in office.
No final pardons
Missing from the pardons list was Libby, the former chief of staff of Dick Cheney, Bush's vice-president.
Bush had commuted Libby's 30-month sentence in 2007, but did not pardon him for lying to a grand jury investigating the leaked identification of CIA operative Valerie Plame.
Also omitted from the list was Ted Stevens, the former Alaska senator, who is fighting his October 27 conviction for failing to report significant gifts on his financial disclosure forms.
Stevens, a Republican, lost his re-election race in November, and has accused federal investigators of misconduct in his case.