The goal umpire on the spot appeared ready to call Guerin's shot touched on the line by a Suns defender, before the decision was sent upstairs.
The "score assist'' review system - introduced this season - eventually confirmed a goal, which put the Blues in front with less than 90 seconds left on the clock.
Gold Coast's Lucy Single had a chance to snatch back the lead in the dying seconds but pushed her shot wide as Carlton hung on for a 5.9 (39) to 5.8 (38) triumph on Sunday in Mackay.
It was the Blues' (1-1) first win of the season and left the Suns (0-2) still searching for their breakthrough after two rounds.
Mimi Hill (23 disposals), Abbie McKay (22) and Keeley Sherar (18) were Carlton's major ball winners, with Guerin one of her side's five single goal-kickers.
Gold Coast star Charlie Rowbottom was busy with 35 disposals, 10 tackles and six clearances, alongside Daisy D'Arcy (25 touches) and Single (23).
The contest was an arm-wrestle from the outset as the teams kicked two goals apiece in both the first and second quarters.
Neither side was able to break open a tight contest in hot, blustery conditions and Gold Coast led by just one point at the main break.
Suns midfielder Claudia Whitfort had been influential with 12 disposals and one goal to that point, but finished the half in the hands of trainers, nursing a left knee injury after a collision with McKay.
Whitfort returned for the third term with the joint strapped as scoring dried up, the Blues turning for home with a one-point advantage after edging ahead with a series of behinds.
Jacqueline Dupuy was shaky in front of goal with 0.3 until she pinned Hill holding the ball and converted, putting the Suns in front midway through the final term.
It looked like it would be the only major of the second half and settle the contest, until Guerin stepped up late for Carlton.
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