A Gary Jones effort after 26th minutes was enough to take Tranmere through to the third round of the FA Cup.
Jones nipped in to score after being picked out by Daniel Harrison's cross from the right.
The goal came barely a minute after Hornchurch's Vinnie John headed into the net only for the effort to be ruled out for a push on Tyrone Loran.
Hornchurch went close when Jon Keeling fired against the post and Tranmere sub Alex Hay also hit the woodwork.
Hornchurch: Gay, Gooding, Kerrigan, Adedeji, West, Locke,
Keeling, John Martin, John Martin, John, McGowan, Graham. Subs:
Opara, Allen, Southon, Rowland, Collier.
Tranmere: Achterberg, Connelly, Tremarco, Loran, Allen,
Linwood, Mellon, Harrison, Beresford, Dadi, Jones. Subs:
Howarth, Taylor, Sharps, Navarro, Hay.
Referee: D Crick (Surrey).