Mediation efforts of Argentina, Brazil, Chile and the United States paved the way for the opening of diplomatic conversations that ultimately led to the signing of a definitive peace agreement (the Brasilia Presidential Act) on 26 October 1998.

One of the outposts causing the dispute, called Tiwintza by the Ecuadorians, and Tiwinza by the Peruvians, came to symbolize the war because of the bitter clashes that took place around it, and the emotional importance that both sides attached to its possession.

The conflict continued until the signing of a ceasefire and the eventual separation of forces, supervised by the MOMEP, a multinational mission of military observers from the "guarantor" countries of the 1942 Rio Protocol: Argentina, Brazil, Chile, and the USA.

Thus, in the aftermath of the war, both nations, brokered by the "guarantors" of the Rio Protocol, entered into a long and difficult negotiation process that concluded with the signing of a Peace Treaty in 1998, and the closing of the hitherto un-demarcated stretch of common border, deep in the Amazonian rainforest.

For the next 46 years, a 78 km-long strip of mostly unpopulated, and little explored territory, deep in the Amazonian rainforest and almost inaccessible by land, was left without a specific boundary; this served as a flashpoint for recurrent diplomatic and military crisis between Ecuador and Peru.

Although the crisis was defused the following month with the signing of a Pacto de Caballeros (gentlemen's agreement), by which both sides committed themselves to abandon these posts and separate their forces, the aftermath of the incident saw both countries accusing each other of violating the accord and reinforcing their military presence in the delimited and undemarcated area.

Apart from the uneasy encounters between rival patrols, which sometimes included brief exchanges of fire, most commonly every January (anniversary of the signing of the Rio Protocol), no serious incidents happened.

The Ecuadorian Army, evidently bent on preventing any repetition of the "Pachacútec" incident, and to forestall any Peruvian attempt to reach to crests of the Condor range, had gone on to establish a "defensive" perimeter on the area of Cenepa valley, with two outposts, "Tiwinza" and "Base Sur", on the Cenepa headwaters (i.e. in the eastern side of the Cordillera del Cóndor, in Peru's land), and a larger outpost, "Coangos", on the high ground overlooking them from the north[1] (see map).

During the second half of December both sides began to hastily reinforce their military presence in and around the Cenepa valley area, laying down new minefields, preparing supply bases, and intensifying the patrolling activity.

By the end of December, profiting from its internal lines of communications, the Ecuadorian Army had strengthened to a considerable degree its presence in the area, having deployed a number of units, foremost among them several Special Forces formations, as well as artillery and BM-21 multiple rocket launchers on the heights of the Cordillera del Cóndor.

The entire Ecuadorian perimeter was covered by antiaircraft batteries and, most significantly, several teams carrying Soviet-made SA-16 Igla and British-made Blowpipe man-portable surface-to-air missiles.

Meanwhile, the Ecuadorian Air Force (FAE) was frantically getting up to operational status its fleet of subsonic and supersonic jet aircraft, and adapting existing airfields in southeastern Ecuador to function as forward-deployment bases.

Troops, heavy weapons, ammunition and supplies had to be flown in first from the Peruvian hinterland and Lima to Bagua AFB, where they were transferred to light transport aircraft for the flight to the Ciro Alegría base.

Following the customary regulations put in place by both armies for the handling of such instances, the so-called Cartillas de Seguridad y Confianza (Guidelines for Safety and Mutual Confidence), the captured Peruvian personnel were delivered to their own officers without further incident.

Thus, as a preliminary to the attack, on 21 January Peruvian helicopters began a series of reconnaissance and troop insertion flights on the rear of the Ecuadorian positions, which continued for the next two days.

That same day, a reinforced Special Forces company was ordered to advance undetected through the dense jungle and dislodge the Peruvians from the site, named by the Ecuadorians' "Base Norte".

On the morning of Thursday, 26 January 1995, after three days of march, the Ecuadorian Special Forces detachment arrived undetected at the small Peruvian outpost "Base Norte" and launched a surprise attack on the unsuspecting garrison.

[26] In a decision that certain political sectors on both sides took as a setback, the Guarantors of the Rio Protocol determined that the boundary of the delimited and undemarcated zone was in fact the Cordillera del Cóndor line, as Peru had been claiming from the 1940s.

While Ecuador was forced to renounce its decades-old territorial claims as Tumbes, Jaen and Maynas as well as on the eastern slopes of the Cordillera, as well as the entire western area of the Cenepa headwaters, Peru "gives" to Ecuador, as a "private property" but without sovereignty and only for commemorative and non-military events, one square kilometer of its territory, in the area where the Ecuadorian base of Tiwinza was located (level 1061), focal point of the war, inside the Peruvian soil, anyone born in Tiwinza will be considered Peruvian.

Both sources agree that Ecuador lost one AT-33A trainer in an accident outside the combat area, three fallen A-37 and two defective Kfir cannot return to the theater of operations in the conflict.

[28] This claim was promptly denied by Chile the following day on February 5, 1995, but admitted that they had sold weaponry to Ecuador on September 12, 1994, as part of a regular commercial exchange that had no aim against any particular nation.

On March 21, 2005, General Bayas was asked by the Ecuadorian newspaper El Comercio if Chile had sold armaments to Ecuador during the Cenepa War, to which he replied: “Yes, it was a contract with the militaries during the conflict.

[28] In this communication, Fernández is reported to have concurred to de Rivero's residence and revealed that only 9mm ammunition, which had been paid with anticipation, had been loaded in the Ecuadorian planes; that a Chilean lawyer representing Ecuador had demanded the fulfillment of the contract and that Ecuadorian military personnel who came on the plane asked for additional armament, only to have this petition denied; however Peruvian Caretas magazine reported that part of this information wasn't precise (without specifying which part).

Peru further claimed that Chile should have maintained absolute neutrality and that this alleged weapons commerce during the Cenepa War went against resolutions made by the United Nations and the Organization of American States.

Quoting Peruvian ambassador to Chile in 1995 (de Rivero), the Chilean Sub-secretary (Fernández) "pointed out to me that President Frei and chancellor (foreign minister) Insulza had been deeply worried by the situation and that they were taking all the dispositions of the case to reform the military sales law".