In-form forward John Dunbar put the Flames ahead after just 28 seconds with the lone goal of the first period, only for visitors Milton Keynes to reply with the sole strike of the second stanza – Kyle Essery the scorer.
The Lightning then claimed a lead of their own just over three and a half minutes into the the third period, Guillaume Doucet providing the finish assisted by Francis Verreault-Paul, Denny Kearney.
But the Flames were not extinguished, Dunbar grabbing his second of the night just under five minutes from the end.
With neither side able to produce a winner in the remaining minutes of regulation or overtime, the game moved to a shootout, Francis Verreault-Paul eventually scoring the decisive goal in the fifth round.
Despite the loss, Guildford are now guaranteed either an automatic qualifying spot as one of the top two teams in Group C, or a wild card spot as one of the two best performing third placed teams, having now secured more points than Dundee Stars managed in Group B.