Play was brought to a halt with quarter of an hour remaining in the second-leg contest after Kiev fans became embroiled in ugly scenes with the team leading 3-1.
Kiev goalkeeper Oleksandr Shovkovskiy attempted to act as peacemaker and pleaded with supporters to stop fighting.
The match did eventually resume, with Kiev holding on to progress 4-3 on aggregate - setting up a last 16 tie with Everton.
However, UEFA has taken a dim view of the incident and the governing body has "ordered the partial closure of FC Dynamo Kyiv Stadium in which they would play as the host club and, in particular, the sector 21 of their stadium."
A fine of €70,000 has also been imposed.
Elsewhere, Roma have been sanctioned for a "late kick-off infringement" in their 2-1 victory Europa League win at Feyenoord.
The Serie A club, who progressed 3-2 on aggregated, have been fined €10,000 - while forward Adem Ljajic has been warned about his future conduct for provoking spectators.
Apparent racial abuse of Gervinho by Feyenoord fans caused delays to the match at De Kuip.
Feyenoord also saw disciplinary proceedings opened against them following the match, the Eredivisie side due to discover their fate on March 19.
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