Aloko reportedly met with the Taliban delegation to discuss terms for a potential peace deal, but only after being explicitly ordered not to hold the meeting by the Karzai administration.
News of the firing comes as unofficial peace talks between Kabul and the Taliban were showing promise.
A secret meeting in Dubai between Mullah Abbas Stanikzai, the lead Taliban negotiator, and members of Karzai's High Peace Council in July reportedly sparked a series of informal discussions between the two sides in recent weeks, The Washington Post reported in August.
Until now, the meetings have been informal in nature and designed to get formal peace talks back on track, according to the Post.
But with Aloko's dismissal on Monday, Karzai seems to be posturing to take full control of any negotiations between Afghanistan, the Taliban and Pakistan.
To that end, Karzai is planning to travel to Pakistan to meet with negotiators there in an attempt to get Islamabad back on board for peace talks with the militant Islamic group.
In April, Pakistan walked away from Afghan-led peace talks with the Taliban, seemingly scuttling any hopes for a pact before U.S. and NATO forces leave Afghanistan in 2014.
Islamabad's demand that Kabul cut all ties with Pakistan's longtime foe, India, as well as immediately sign a military cooperation pact with Pakistan was too much to ask, Afghan officials said at the time.
However, the Karzai administration has also provided many of their own roadblocks to peace with the Taliban.
In June, the Obama administration announced that they would begin direct talks in Qatar with Taliban representatives. That decision coincided with the official handover of security operations from U.S. and allied forces to Afghan troops.
Bu the White House's efforts to take the lead on any Taliban peace negotiation sparked outrage from Karzai’s government, which suspended talks with the U.S. on plans for a post-war security deal.
Prior to announcing the Taliban talks, U.S. officials had said Kabul would take the lead in peace negotiations with the terror group, working off a plan drafted by the Karzai administration.
While it remains to be seen whether Karzai's latest gambit to revitalize the peace talks will work, bringing the Taliban to the negotiation table will be integral to the American handover of security operations to Afghan forces over the next year, according to the top U.S. commander in the country.
Forging a peace plan with the Taliban is critical to gaining that stability, ahead of the 2014 withdrawal deadline for all U.S. and coalition forces from the country, according to Gen. Joseph Dunford, the top commander for all U.S. forces in Afghanistan.
"That really is the focus of effort over the next 18 months. That's why we need to start now — especially with the Afghan security forces — to talk about 2018, not 2014," the four-star general told the BBC in June.
"That period of time will allow these gains to be sustainable," he added.