Second-placed Chelsea closed the gap back to 10 points with a 4-0 thrashing of Birmingham City Ladies.
City dominated a scoreless first half against Reading but had to wait until Beattie's second-half header to lead.
Houghton's classy late free-kick found the bottom corner to make it 2-0.
The victory was well deserved but the visitors restricted City's opportunities in the first period, with Jane Ross going closest when her shot hit the bar.
However, Beattie eased any fears of dropping points when she converted Toni Duggan's free-kick soon after the restart, and fellow centre-back Houghton wrapped up victory with two minutes remaining.
City have three league matches left, including one against Chelsea. Even if they lose to the London side, City need only two wins to be certain of clinching the league title.
Manchester City defender Jennifer Beattie:
"I know the feeling of having won the league and I want that to happen with this club. It's a brilliant club and we want titles, and we want silverware. Hopefully experience will help.
"The best thing is that we're still not happy; we still think we can get better.
"We've scored twice from set pieces but we want to be scoring from open play too. We've got the quality there but it's just about making it happen in the final third."
Reading defender Molly Bartrip:
"It's difficult to be sat back in your own half, but you come away to teams like Manchester City and you expect that.
"We knew what we had to do to stop them getting through us. We executed it really well, it was just two silly set pieces.
"I think if you look at both games between the two teams, we have matched them both times. It's little mistakes that are costing us the game."
Match ends, Manchester City Women 2, Reading Ladies 0.
Second Half ends, Manchester City Women 2, Reading Ladies 0.
Foul by Georgia Stanway (Manchester City Women).
Remi Allen (Reading Ladies) wins a free kick in the defensive half.
Substitution, Manchester City Women. Georgia Stanway replaces Jill Scott.
Goal!  Manchester City Women 2, Reading Ladies 0. Stephanie Houghton (Manchester City Women) from a free kick with a right footed shot to the bottom left corner.
Jane Ross (Manchester City Women) wins a free kick in the attacking half.
Foul by Kirsty McGee (Reading Ladies).
Corner,  Manchester City Women. Conceded by Rebecca Jane.
Foul by Keira Walsh (Manchester City Women).
Emma Follis (Reading Ladies) wins a free kick in the attacking half.
Attempt blocked. Toni Duggan (Manchester City Women) right footed shot from outside the box is blocked.
Foul by Keira Walsh (Manchester City Women).
Lauren Bruton (Reading Ladies) wins a free kick in the defensive half.
Attempt missed. Nikita Parris (Manchester City Women) right footed shot from the centre of the box is just a bit too high following a fast break.
Foul by Demi Stokes (Manchester City Women).
Remi Allen (Reading Ladies) wins a free kick on the right wing.
Foul by Demi Stokes (Manchester City Women).
Rachel Rowe (Reading Ladies) wins a free kick on the left wing.
Attempt missed. Nikita Parris (Manchester City Women) header from the left side of the six yard box is close, but misses the top left corner.
Foul by Keira Walsh (Manchester City Women).
Lauren Bruton (Reading Ladies) wins a free kick in the attacking half.
Foul by Jennifer Beattie (Manchester City Women).
Molly Bartrip (Reading Ladies) wins a free kick in the attacking half.
Attempt saved. Stephanie Houghton (Manchester City Women) right footed shot from outside the box is saved in the centre of the goal.
Substitution, Reading Ladies. Melissa Fletcher replaces Jade.
Jane Ross (Manchester City Women) wins a free kick in the attacking half.
Foul by Kylie Davies (Reading Ladies).
Attempt blocked. Nikita Parris (Manchester City Women) right footed shot from outside the box is blocked.
Keira Walsh (Manchester City Women) wins a free kick in the attacking half.
Foul by Rachel Rowe (Reading Ladies).
Corner,  Manchester City Women. Conceded by Harriet Scott.
Nikita Parris (Manchester City Women) wins a free kick on the left wing.
Foul by Kirsty McGee (Reading Ladies).
Foul by Jill Scott (Manchester City Women).
Remi Allen (Reading Ladies) wins a free kick in the defensive half.
Substitution, Manchester City Women. Nikita Parris replaces Daphne Corboz.
Foul by Jill Scott (Manchester City Women).
Molly Bartrip (Reading Ladies) wins a free kick in the attacking half.
Corner,  Manchester City Women. Conceded by Mary Earps.
Jennnifer Beattie and Steph Houghton scored as Manchester City briefly stretched their lead at the top of the Women's Super League to 13 points with a patient victory over winless Reading.