The Bukhoro (Bukhara) Khanate then lost the crucial Samarqand area to Russian forces in 1868. To avoid alarming Britain, which had strong interests in protecting nearby India, Russia left the Bukhoran territories directly bordering Afghanistan and Persia nominally independent. The Central Asian khanates retained a degree of autonomy until 1917.
The geographic isolation of Central Asia slowed the southward advance of Russian forces, but Bukhara was invaded in 1868
Eventually Kaufman realized that the Emir, once again, was stalling for time. Thus on December 19, he wrote to the Bokharans asking that Muzaffar ratify the peace, treaty and that the captive Russian soldiers be returned to Tashkent. To make sure that he need only fight on one front, Kaufman concluded a treaty with Kokand in 1868, effectively making the Khan a vassal of the Tsar.
While Kaufman prepared for war, Muzaffar al-Din's position was becoming shakier. The ulema criticized him for even talking to the Russians and threatened to replace him with his eldest son. Further, the Emir managed to alienate the Uzbek aristocracy by curbing their raiding.
Finally in late March 9,1868, the Bokharan war party, composed of ulema, hakims, and merchants, proclaimed a ghazawat, or holy war, to defend country and religion against the Russian infidel. In Samarkand the garrison had to be called out to restore order after the mullahs had roused the populace to a jihad. In Bokhara the Emir was forced to flee from his capital to Kermine, where he finally gave in to the war hawks and himself proclaimed a ghazawat. By mid-April the Bokharan army, led by the Emir in person, was moving toward the Zarafshan River.
Kaufman learned of these developments on April 8, 1868. Even though war preparations had continued, the March release of the imprisoned Russians had breathed hope into the prospects for a peaceful settlement. The subsequent declaration of a holy war and the buildup of Bokharan forces at Samarkand finally caused the Russian government to approve an expedition against the emirate.
When the Emir refused to move his army away from the Zarafshan River, Kaufman marched into Bokharan territory. Samarkand fell on May 2 after the Russians had routed the Bokharan host outside the city gates the previous day. With a 700 man garrison left in Timur's ancient capital, Kaufman pushed on after the Bokharan army. Urgut was taken on May 14 and Katta-Kurgan four days later. After. the Russians occupied the, latter, they once again sent a peace proposal to Muzaffar, who rejected the offer and dealt harshly with the two Persians who had conveyed it.
Finally on June 2, following the rejection of the latest peace offer, the Bokharans turned to fight. They occupied the Zerbulak Heights overlooking Katta-Kurgan and entrenched the site. Some 6,000 Sarbaz, 14 guns, and 15,000 Sipahis were dug in and waiting for the Russians. Without hesitation, Kaufman sent his 3,500 men up the slopes. The Bokharans were routed, having suffered lost a cost of 38 wounded, the governor-general had broken the back of the Bokharan army and opened the way to the city of Bokhara.
Despite this situation, Kaufman was unable to exploit his success. Not long after the Bokharans had fled the field, word reached him that the garrison at Samarkand was in desperate condition. On June I the city had risen against the Russian garrison, which managed to gain the citadel. 700 Russian soldiers, commanded by one Major Shtempel, were set upon by overwhelming numbers: 15,000 Samarkandians; 15,000 other Bokharans and Khazaks; and 25,000 men from the semi-autonomous Bokharan province of Shahr-i-Sabz.
Kaufman quickly turned his army around and marched to relieve the beleaguered garrison. When his troops lifted the siege on June 8, they discovered how near had been disaster. Shtempel's men were running out of supplies and ammunition and were nearing physical exhaustion.
Ten days after Samarkand was relieved, Muzaffar capitulated and asked for peace terms. Paying an indemnity; losing Samarkand, Katta-Kurgan and neighboring territories; and conceding trade rights to the Russians, the Emir realized he merely postponed the inevitable. In September, 1873, Bokhara officially became a Russian protectorate.