The victory was Rowntrees’ best away win in the league for more than a year.
Stewart’s opening goal for Rowntrees was cancelled out by former York City midfielder Christian Fox.
However, before the break, Stewart restored the visitors’ lead and Dan Marshall added a third for Rowntrees.
In a second half dominated by the visitors, Stewart took his personal tally for the game to four and Marshall added his second of the afternoon.
In the sole division four game to survive the downpours, Melbourne recorded their first home win over LNER Builders since they rejoined the league in 2005.
Brian Underwood gave Melbourne the lead at the break and, although the Builders levelled on the hour mark, Paul Watson hit the winner only ten minutes later.
It was only the third time that Melbourne had beaten the Builders in their previous 16 league meetings.
Old Malton St Mary’s hit five goals past Riccall for the second time this season in reserve ‘A’.
The Ryedale side followed up their 5-3 win at Riccall three weeks ago by defeating the same opposition 5-0 on Saturday.
The Ryedale side took control of the game early on with goals from Neil Wilford, Richard Cass, Dean Leadill and Dean Clarkson before Richard Stevenson completed the scoring in the second half. In reserve ‘C’, Tockwith ended a six-match winless run with a 4-3 victory at Rowntrees. The hosts had the perfect start as Steve Ward struck twice in the opening half an hour.
However, the next 30 minutes were bossed by the visitors, who replied through Steve Dey, Simon Lewis and John Richardson to lead 3-2.
Shaun Stewart briefly restored parity but Dey’s second goal of the afternoon clinched a fourth win on the trot for Tockwith over Rowntrees’ second string.
The weather also played havoc with the York FA cup matches.
The only tie played saw Sporting Knavesmire win 2-1 at Selby Town Reserves in round three of the York FA Saturday Junior Cup.
Trailing 1-0 at the break, Sporting quickly equalised through Jonny Brown. George Wilson headed in the winner 20 minutes from time.
Knavesmire host Bishopthorpe United in round four on Saturday, January 5 (1.30pm).