Byron Moore should have put Crewe ahead after just 12 minutes but his poor shot was deflected for a corner by the foot of defender Terrell Forbes.
Both teams struggled to create any openings in a dull opening half-hour but the Alex almost netted when Dennis Lawrence's shot took a wicked deflection off Paul Warne. Luckily for the Glovers striker the ball span just over his own crossbar.
However, the Railwaymen took the lead just before half-time. Wagenaar could only punch Billy Jones' corner into the path of Moore on the edge of the box and the winger's well-controlled side-footed shot was turned in by Donaldson.
Wagenaar kept his team in it after the break with a superb finger-tip save to deny Donaldson's goalbound header before he kept out the same player with another good stop when one-on-one.
But the keeper's good work was undone when he failed to hold on to John Brayford's harmless 79th-minute cross and somehow turned the ball into his own net.