The win, Baroda's second in three matches, helped the defending champions pocket four points and are now level with Saurashtra at eight points. Both the teams have a game in hand.
Chasing a modest 134 for victory, Baroda lost Kedar Devdhar off the first ball of the innings when he caught by wicket-keeper Sheldon Jackson off left-arm pacer Jaydev Unadkat.
Irfan Pathan (12), who came in next, too departed early but Waghmode hit eight boundaries and two sixes in his unbeaten 66-run knock and along with Jyot Chhaya (1 not out) took Baroda home without losing any more wickets.
For Saurashtra, Unadkat took two wickets conceding 22 runs and Siddharth Trivedi chipped in with a wicket for 26 runs.
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Earlier, put into bat first, Saurashtra got off to a good start but failed to capitalise on it and were restricted to 133 for eight in 20 overs.
Shah was caught and bowled by leg-spinner Hardik Pandya for 45-ball 49, which included five hits to the fence and two over it.
The West Zone league of the tournament is now nicely poised. If Saurashtra beat Gujarat and Baroda beat Maharashtra tomorrow, there will be a three-way tie among Gujarat, Baroda and Saurashtra, following which net run-rate will come into play.