Root struck again as Chris Cooke mistimed a drive and bottom-edged onto his stumps for eight, and Tom Bevan almost played on first ball.
Yorkshire kept switching their bowlers and kept their hopes alive as Bevan fell lbw for 12 to occasional spinner Lyth on the last ball before tea.
Lyth struck again after the interval when James Harris was given out leg-before despite appearing to be struck outside off-stump, but at 16:18 BST a flash of lightning obliged the umpires to take the players off.
With thunder in the area and dark clouds overhead, the match was finally abandoned at 16:59 BST moments before the rain arrived.
Glamorgan next face Sussex on Friday 10 May while Yorkshire have a bye week before travelling to Hove to face the same opponents.