Dinamo controlled possession early on but struggled to carve out clear cut chances with Semshov well off target from distance and Kokorin's effort blocked by Sean Dillon.
Visiting captain Kuranyi took a fresh air swipe at the ball after being found in a promising position but the striker made a better connection moments later, his header from Zvjezdan Misimovic's cross sneaking past the post.
The hosts then scored against the run of play as John Rankin's shot deflected into the path of Flood and the midfielder's composed finish found the net with the aid of the post.
Suddenly Dundee United had a foothold in the match and skipper Jon Daly should have doubled their lead with a headed chance.
Flood's searching ball found last season's club top scorer at the back post but the big striker nodded wide.
United continued where they left off with a positive start to the second half but they were undone when Gavin Gunning conceded possession and Kokorin soon crossed for the unchallenged Semshov to head home.
Impressive debutant Cierzniak blocked from Kuranyi twice in quick succession and Kokorin and Misimovic were also frustrated by the Polish keeper.
At the other end, Rankin's powerful drive slipped past and Gary Mackay-Steven's crosses caused problems for Dinamo keeper Anton Shunin, with one delivery touched onto the post.
But the pressure told when Watson forced the ball past Shunin after Gunning's header and Daly's effort had been blocked as Dinamo were caught out at Mackay-Steven's corner.
United continued to press when they could while the Russians maintained their attacking threat.
And Houston's side were dealt a heart-breaking blow when Kokorin's shot from the edge of the box was diverted over Cierzniak by a United defender.
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