Peter Crouch's 29th-minute volley had England deservedly ahead at Wembley. Andriy Shevchenko came off the bench to equalise after 74 before Terry swept in the winner following a free kick from substitute David Beckham.
It was a far from impressive victory but the hosts will care little after making it five qualifying wins out of five.
England lead the group on 15 points. Croatia are second on 10 after they won 2-0 in Andorra on Wednesday, with Ukraine third on seven points.
The home team crushed Slovakia 4-0 in a friendly on Saturday but were a little subdued in the opening quarter, a speculative Wayne Rooney overhead kick and a fizzing Steven Gerrard shot the best they could conjure.
The opening goal was a simple one as Terry nodded a Frank Lampard corner into the path of Crouch, who hooked it home from six metres.
Crouch had been selected only because of injuries to Emile Heskey, Carlton Cole and Darren Bent. Wednesday's goal was his 15th in 33 internationals, though his first under coach Fabio Capello and his first for England since November 2007.
LITTLE AMBITION
Ukraine, unbeaten in their opening three qualifying games, showed precious little ambition.
The visitors barely threatened in the first half but almost equalised when a long-range effort from captain Anatoliy Tymoschuk took a wicked bounce and was kept out by the shoulder of a startled David James in goal.
Shevchenko came on for Andriy Voronin after 55 minutes to earn a record 86th cap.
His AC Milan team mate Beckham, England's most-capped outfield player, joined the fray soon after to claim his 110th cap but England lost their way and meandered through much of the second half.
Capello's men paid the price when Olexandr Aliev's free kick hit the chest of a flat-footed Glen Johnson and Shevchenko reacted instantly to lash the ball home.
England immediately upped the tempo but had to rely on the dead-ball delivery of Beckham to get them out of jail.
He swung in a free kick from the right which Gerrard knocked back across the face of goal for Terry to stretch out a leg and score.
The result leaves England ideally placed to make it to the 2010 finals in South Africa and they can expect two more wins from their next games, in Kazakhstan on June 6 and at home to Andorra four days later.
Ukraine next visit Croatia before hosting Kazakhstan.
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