Bowen struck after 25 and 58 minutes to inflict a first home defeat upon Leeds since September 22 as in-form Tigers extended their unbeaten sequence to seven matches in impressive fashion.
Leeds could have few complaints at the scoreline in a game in which they failed to hit the heights of their fantastic seven-match winning streak and failed to score on home soil in the league for just the second time this season.
Leeds, who produced little flow to their play, were far from at their best in the first period with Hull deserving of plaudits after making light of the absence of three key players in Tommy Elphick, Jackson Irvine and Fraizer Campbell.
It was announced ahead of the game that loan defender Elphick had returned to parent club Aston Villa, while Irvine was missing due to forthcoming international commitments with Australia and top-scorer Campbell absent through injury.
The cards were seemingly all stacked against Hull, but they creditably dusted themselves down and produced a highly accomplished away-day showing in the first half.
Strong and organised at the back, alert in midfield and with a distinct threat going forward, Hull deservedly led thanks to Bowen's low strike, with the winger profiting after Leeds failed to clear their lines following Kamil Grosicki's free-kick.
Grosicki was also a whisker away from turning in Todd Kane's dangerous low cross with the Polish winger also raising a few flutters early on when his free-kick flew into the side-netting.
Palblo Hernandez was at the heart of the hosts' best efforts and after firing a half-volley over early on, the Spaniard went as close as anyone to levelling with his stinging drive palmed away by David Marshall.
Leeds threw on youngster Jack Clarke at the start of the second half in their bid to wrestle back the initiative and despite more tempo and pressure, the killer development came from Hull.
Grosicki got away from Barry Douglas and after seeing his cross-shot parried, Bowen turned in the rebound to take his season's tally to ten goals.
Luke Ayling went close to pulling one back with a header which was cleared off the line by Jon Toral, with Kane also alert to clear away a goalbound effort from Tyler Roberts on an afternoon which belonged to Hull - who recorded their fourth successive win.
Leeds United: Peacock-Farrell; Ayling (Shackleton 77), Jansson, Phillips, Douglas (Roberts 64); Forshaw, Klich, Harrison (Clarke 45); Alioski, Hernandez, Roofe. Substitutes unused: Huffer, Shackleton, Halme, Davis, Baker.
Hull City: Marshall; Kane, Burke, De Wijs, Kingsley; Henriksen, Stewart; Bowen, Evandro (Toral 45), Grosicki (Lichaj 74); Keane (Batty 90). Subs: Long, Dicko, McKenzie, Martin.
Referee: John Brooks (Leicestershire).