Brentford's 1-0 victory at Blackburn Rovers on Saturday (AEDT) had put the Bees into second place in the Championship.
The tight nature of the race for automatic promotion was encapsulated when Swansea City climbed to second after a 1-0 win at Luton Town in the day's early kick-off.
But Watford ended the day back in second place, above the Swans on goal difference.
Francisco Sierralta's early own goal was cancelled out by a solo strike from Watford's Nathaniel Chalobah before Masina smashed in a last-gasp free-kick.
Watford is three points clear of fourth-placed Brentford, but has played a match more than both promotion rivals below.
At Kenilworth Road, Conor Hourihane's goal after three minutes proved enough for Swansea to record a third victory from four matches.
Barnsley maintained its impressive form with a 3-2 win at Bournemouth.
The Tykes, who had won seven straight games before the midweek draw against Derby County, went ahead in the 16th minute through Michal Helik.
Arnaut Danjuma hauled Bournemouth level in the 22nd minute before Dominic Solanke put the Cherries in front on the stroke of half-time.
Barnsley equalised on the hour through Dominik Frieser and with nine minutes left, Carlton Morris's header lifted Valerien Ismael's sixth placed side five points clear of seventh placed Bournemouth.
Fifth placed Reading hit back to draw 1-1 at Nottingham Forest.
Forest took the lead four minutes into the second half when Royals defender Tom Holmes turned a cross from Sammy Ameobi into his own net.
However, Reading's pressure told when Yakou Meite fired in an equaliser with just nine minutes left.
Bottom of the table Wycombe Wanderers beat Preston North End 1-0, while Bristol City won 3-0 at struggling Birmingham City.
Millwall won 1-0 at Derby, with Shaun Hutchinson heading in from a corner just before half-time.
Middlesbrough beat Stoke City 3-0 to keep alive its faint play-off hopes and Juninho Bacuna's goal gave Huddersfield Town a 1-0 win at Queens Park Rangers.