The firm beat 175 entrants to win the accolade, which was awarded by First Tuesday, the networking forum for technology entrepreneurs and investors, in conjunction with Internet World.
Shipserv is a maritime e-marketplace that helps buyers and sellers of ship supplies to reduce the costs associated with doing business together.
The panel of judges included business leaders from Google, Intel and Cisco, which commended Shipserv for its innovation, growth rate and future potential.
Christer Holloman, chief executive of First Tuesday, said: "Despite the economic doom-and-gloom, entrepreneurialism in web-based companies continues to thrive in the UK, and in London in particular.
"What largely disappeared after the dot-com bust of 2000 has re-emerged, with a vibrant mix of young start-ups and experienced venture capitalists fighting against the recession with innovative thinking and solid business planning."