Following their 1-0 defeat to Levadia Tallinn and 2-1 victory over hosts Zenit Saint Petersburg, Ashgabat needed to take all three points against the seven-time Moldovan champions to guarantee they would join Pakhtakor in the quarter-finals.
However, their heavy loss meant that they were eliminated from the tournament along with the two other Asian sides Dordoi Dynamo and Regar-TadAZ, both of whom failed to pick up a single point.
Kyrgyzstan’s Dordoi Dynamo lost their third and final Group C match as the two-time AFC President’s Cup winners went down 2-0 to Serbians OFC Belgrade, while six-time Tajikistan champions Regar-TadAZ left with the worst record of all 16 teams in the group stage following their 5-1 defeat at the hands of Lithuanian side FBK Kaunas.
With two wins from their opening two games Pakhtakor had already booked their place in the last eight and still managed to top Group D despite losing 2-1 to BATE Borisov from Belarus.
The Uzbek giants continue the defence of their CIS trophy on Wednesday when they take on FK Ventspils from Latvia, in a repeat of the 2007 final.