Cory Paterson broke the line before putting Bowen through towards the tryline but the fullback was brought down 10m out by Panthers halfback Luke Walsh, who then subsequently gave away a penalty after appearing to take exception to comments by Glenn Hall.
Walsh was placed in the sin bin and Segeyaro made the most from the resulting penalty, crossing from dummy half.
On 36 minutes, Bowen dropped Panthers debutant Harry Seijka's chip and Nathan Smith collected before playing out wide where winger Adrian Purtell crossed to regain Penrith's lead.
The Panthers played the second half without lock Luke Lewis, who was knocked unconscious and cut his temple after slamming his head on the ground while diving for the ball in the Cowboys in-goal on the halftime buzzer.
The Cowboys were the first to strike after halftime, taking advantage of a Panthers mistake after the kickoff and Ashton Sims stretched out to even the score.
The North Queensland side took the lead nine minutes later after another dummy half effort by Segeyaro.
The Cowboys needed to win by eight points or more to put themselves back above the Broncos on the ladder and Brent Tate helped them to a 10 point advantage in the 60th minute, out-jumping Ryan Walker to get his hands on a Bowen bomb.
Walker was again beaten moments later when Ash Graham collected a Bowen chip and swivelled past him to score the Cowboys' fourth second-half try. Ray Thompson ensured the Cowboys home-final dreams were kept alive with a try in the 78th minute.
Cowboys 30 (J. Segeyaro 2, A. Graham, A. Sims, B. Tate, R. Thompson tries; M. Bowen 3 goals) Panthers 18 (A. Purtell 2, B. Tighe tries; L. Walsh 2, H. Seijka goals)
